- modeller_usage - salilab.org

to model heterodimer protein of mossing residue
by Arun Dhanasekaran 31 Aug '23

31 Aug '23

i tried a build a homology model of a heterodimer protein,since it contains missing residue i have to model that. But i am only familiar with single chain homology modelling and fro multi chain i am getting many errors like in greeting ali flie. and from tutorial also i am not getting everything clearly. can i get a detailed explantiojn on multi chain modelling

3 4

generate a psf file
by sedmo.info＠gmail.com 08 Aug '23

08 Aug '23

Dear all, I have used modeller to generate a pdb file. unfortunately, the pdb file is not regular as the columns 10 and 11 interfere. What can I do? I can not use the pdb file to generate a psf file.

2 1

Homodimer modelling
by g.m.tuveri＠gmail.com 26 Jul '23

26 Jul '23

Hello, I'm trying to add some missing domains to a big homodimeric protein, pdb 8em4. I predicted the missing structures with Alphafold and now I want to create an entire model of 8em4 using multiple templates. I am using the following directives: # Comparative modeling by the AutoModel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the AutoModel class log.verbose() # request verbose output class MyModel(AutoModel): def special_restraints(self,aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = Selection(self.chains['A']).only_atom_types('CA') s2 = Selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(Symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) env = Environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.'] a = MyModel(env, alnfile = 'ali_lrp2.ali', # alignment filename knowns = ("8em4","domain1","domain2","domain3"), # codes of the templates sequence = 'A0A6P5R9N9') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual comparative modeling In ali_lrp2.ali I have aligned the entire lrp2 sequence with the known 8em4 sequence for the two monomers. Headers are the following: >P1;A0A6P5R9N9 sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00 >P1;8em4 structureX:8em4:28:A:4414:B::: 2.83:-1.00 I don't report the sequences, but for each of the headers I am separating the two monomers with a /, for example >P1;A0A6P5R9N9 sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00 AAAAAAAAAAAAAAAAAAAA/ BBBBBBBBBBBBBBBBBBBB* >P1;8em4 structureX:8em4:28:A:4414:B::: 2.83:-1.00 AAAAAA-----AAA-AAAAA/ BBBBBB-----BBB-BBBBB* Then I add the missing domain template sequence in the following way: >P1;domain1 structureX:domain1::A::B:::: ------AAAAA---------/ ------BBBBB---------* >P1;domain2 structureX:domain2::A::B:::: --------------A-----/ --------------B-----* I keep obtaining knots, especially in the long domain. I made sure that the alignment is correct, but maybe the request of symmetry or the use of multiple templates are badly implemented. I attach the long alignment file >P1;A0A6P5R9N9 sequence:A0A6P5R9N9:1:A:9322:B:::-1.00:-1.00 MERGAAAAAAWMLLLAIAACLAPVSGQECGSGNFRCDNGYCIPASWRCDG TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE QQNCPGTTCSSQQLTCSNGQCVPIEYRCDHVSDCPDGSDERNCYYPTCDQ LTCANGACYNTSQKCDHKVDCRDSSDEANCTTLCSQKEFQCGSGECILRA YVCDHDNDCEDNSDEHNCNYDTCGGHQFTCSNGQCINQNWVCDGDDDCQD SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDENN ATSGRYCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD DCQIWGICDQKCENRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQSKVFS TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDTD EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA QHSTVFYSDLSKDIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW TDGGLKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSASRLYWVDAFFDKIEHSNLD GLDRKRLGHVDQMTHPFGLTVFEDNVFLTDWRLGAIIRVRKSDGGDMTVV RSGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC PYGMKLQRDQMTCEGDPAREPPTQQCGSFSFPCNNGKCVPSIFRCDGVDD CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ NCPTHSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW ECDGHPDCIQGSDEHNGCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC NQDSCSHFNGGCTHQCMQGPFGATCVCPIGYQLANDTKTCEDVNECDTPG FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLAVASRDKIVV DNITAHMHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLQGKTWSAFQNGT DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRKQVIASDLVLHHPHAL TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVHQPLGIIAIHPSRQP SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL MSVRENVIFGISLDPEVKSNDAMVPISGIHHGYDVEFDDSEQFIYWVENP GEIHRVKTDGSNRTVFAPLSLLGSSLGLALDWISKNIYYTTPASRSIEVL TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA KIASANMDGTSLKILFTGNMDHLEVVTLDIQEQKLYWAVTSRGVIERGNV DGTERMILVHHLAHPWGLAVHGSYLYYSDEQYEVIERVDKSSGSNKVVFR DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG FKLSPDGRSCSPYNSFMVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR KVFQASKQPGNTDPPTVIRDNINLLRDVTIFDEHVQPLSPAELNNNPCLQ SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL RSLHFDPQDHNLPFQAISVEGTAIALDYDRRNNRIFFTQKLNPIRGQISY VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVIVSTAFHSFGL TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA RCNQFQFTCLNGRCITQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC ANGRCVPYHYRCDFYNDCGDNSDEAGCLFRSCNSTTEFTCSNGRCIPLSY VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQFTCQNGQCITK LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK RTCVDIDECKESPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI EPYLIFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEKRLYWIDAE KQIIERMFLNKTNRETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS DLEGRQRRMLAQHCVDANNTFCFENPRGIVLHPQRGHVYWADWGDKAYIA RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFRCNNGRC IPQSWKCDVDNDCGDYSDEPTHECMTAAYNCDNHTEFSCKTNYRCIPQWA VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF ECKNHVCIQSFWICDGENDCVDGSDEEIHLCFNVPCESPQRFRCDNSRCI YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFKP STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQTIDYDWDPEGIG LSVVYYTVLAQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNDDRIYWS DSKEDVIESIKYDGTDRRLIINEAMKPFSLDIFEDQLFWVAKEKGEVWRQ NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP KCKCSSGYSGEYCEIGLSRGIPPGTTMAVLLTFVIVIIVGALVLVGFFHY RKTGSLLPSLPKLPSLSSLAKPSENGNGVTFRSGADVNMDIGVSPFGPET IIDRSMAMNEHFVMEVGKQPVIFENPMYAAKDSTSKVGLAVQGPSVSSQV TVSENVENQNYGRSVDPSEIVPEPKPASPGADETQGTKWNIFKRKPKQTT NFENPIYAEMDTEQKEAVAVAPPPSPSLPAKASKRSSTPGYTATEDTFKD TANLVKEDSDV/ MERGAAAAAAWMLLLAIAACLAPVSGQECGSGNFRCDNGYCIPASWRCDG TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE QQNCPGTTCSSQQLTCSNGQCVPIEYRCDHVSDCPDGSDERNCYYPTCDQ LTCANGACYNTSQKCDHKVDCRDSSDEANCTTLCSQKEFQCGSGECILRA YVCDHDNDCEDNSDEHNCNYDTCGGHQFTCSNGQCINQNWVCDGDDDCQD SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDENN ATSGRYCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD DCQIWGICDQKCENRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQSKVFS TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDTD EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA QHSTVFYSDLSKDIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW TDGGLKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSASRLYWVDAFFDKIEHSNLD GLDRKRLGHVDQMTHPFGLTVFEDNVFLTDWRLGAIIRVRKSDGGDMTVV RSGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC PYGMKLQRDQMTCEGDPAREPPTQQCGSFSFPCNNGKCVPSIFRCDGVDD CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ NCPTHSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW ECDGHPDCIQGSDEHNGCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC NQDSCSHFNGGCTHQCMQGPFGATCVCPIGYQLANDTKTCEDVNECDTPG FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLAVASRDKIVV DNITAHMHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLQGKTWSAFQNGT DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRKQVIASDLVLHHPHAL TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVHQPLGIIAIHPSRQP SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL MSVRENVIFGISLDPEVKSNDAMVPISGIHHGYDVEFDDSEQFIYWVENP GEIHRVKTDGSNRTVFAPLSLLGSSLGLALDWISKNIYYTTPASRSIEVL TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA KIASANMDGTSLKILFTGNMDHLEVVTLDIQEQKLYWAVTSRGVIERGNV DGTERMILVHHLAHPWGLAVHGSYLYYSDEQYEVIERVDKSSGSNKVVFR DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG FKLSPDGRSCSPYNSFMVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR KVFQASKQPGNTDPPTVIRDNINLLRDVTIFDEHVQPLSPAELNNNPCLQ SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL RSLHFDPQDHNLPFQAISVEGTAIALDYDRRNNRIFFTQKLNPIRGQISY VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVIVSTAFHSFGL TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA RCNQFQFTCLNGRCITQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC ANGRCVPYHYRCDFYNDCGDNSDEAGCLFRSCNSTTEFTCSNGRCIPLSY VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQFTCQNGQCITK LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK RTCVDIDECKESPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI EPYLIFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEKRLYWIDAE KQIIERMFLNKTNRETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS DLEGRQRRMLAQHCVDANNTFCFENPRGIVLHPQRGHVYWADWGDKAYIA RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFRCNNGRC IPQSWKCDVDNDCGDYSDEPTHECMTAAYNCDNHTEFSCKTNYRCIPQWA VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF ECKNHVCIQSFWICDGENDCVDGSDEEIHLCFNVPCESPQRFRCDNSRCI YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFKP STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQTIDYDWDPEGIG LSVVYYTVLAQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNDDRIYWS DSKEDVIESIKYDGTDRRLIINEAMKPFSLDIFEDQLFWVAKEKGEVWRQ NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP KCKCSSGYSGEYCEIGLSRGIPPGTTMAVLLTFVIVIIVGALVLVGFFHY RKTGSLLPSLPKLPSLSSLAKPSENGNGVTFRSGADVNMDIGVSPFGPET IIDRSMAMNEHFVMEVGKQPVIFENPMYAAKDSTSKVGLAVQGPSVSSQV TVSENVENQNYGRSVDPSEIVPEPKPASPGADETQGTKWNIFKRKPKQTT NFENPIYAEMDTEQKEAVAVAPPPSPSLPAKASKRSSTPGYTATEDTFKD TANLVKEDSDV* >P1;8em4 structureX:8em4:28:A:4414:B:MOL_ID 1; MOLECULE LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN CHAIN A, B; SYNONYM LRP-2,GLYCOPROTEIN 330,GP330,MEGALIN:MOL_ID 1; ORGANISM_SCIENTIFIC MUS MUSCULUS; ORGANISM_COMMON HOUSE MOUSE; ORGANISM_TAXID 10090: 2.83:-1.00 ----------------------------CGSGNFRCDNGYCIPASWRCDG TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE QQNC---------------------------------------------- -------------------------------------------------- --------------------DTCGGHQFTCSNGQCINQNWVCDGDDDCQD SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDE-- -----YCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD DCQIWGICDQKCESRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQAKVFS TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDAD EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA QHSTIFYSDLSKNIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW TDGGSKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSTSRLYWVDAFFDKIEHSNLD GLDRKRLGHVDQMTHPFGLTVFKDNVFLTDWRLGAIIRVRKSDGGDMTVV RRGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC PYGMKLQRDQMTCEGDPAREPPTQQCGSSSFPCNNGKCVPSIFRCDGVDD CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ NCPTRSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW ECDGHPDCIQGSDEHNGCVPKT---------------------------- -------------------------------------------------- NQDSCLHFNGGCTHRCIQGPFGATCVCPIGYQLANDTKTCEDVNECDIPG FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLVVASRDKIIM DNITAHTHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLEGKTWSAFQNGT DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRRQVIASDLVLHHPHAL TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVPQPLGIIAIHPSRQP SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL ISVRENVIFGISLDPEVKSNDAMVPISGIQHGYDVEFDDSEQFIYWVENP GEIHRVKTDGSNRTAFAPLSLLGSSLGLALDWVSRNIYYTTPASRSIEVL TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA KIASANMDGTSLKILFTGNMEHLEVVTLDIQEQKLYWAVTSRGVIERGNV DGTERMILVHHLAHPWGLVVHGSFLYYSDEQYEVIERVDKSSGSNKVVFR DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG FKLSPDGRSCSPYNSFIVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR KVFQASKQPGNTDPPTVIRDSINLLRDVTIFDEHVQPLSPAELNNNPCLQ SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL RSLHFDPQDHNLPFQAISVEGMAIALDYDRRNNRIFFTQKLNPIRGQISY VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVVISTAFHSFGL TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA RCNQFQFTCLNGRCISQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC ANGRCVPYHYRCDFYNDCGDNSDEAGCLF--------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------------------------------CRDDQFTCQNGQCITK LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK RTCVDIDECKETPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI EPYLVFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEERLYWIDAE KQIIERMFLNKTNQETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS DLEGRQRKMLAQHCVDANNTFCFENPRGIVLHPQRGYVYWADWGDHAYIA RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFKCNNGRC IPQSWKCDVDNDCGDYSDEPIHECMTAAYNCDNHTEFSCKTNYRCIPQWA VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF ECKNHVCIQSFWICDGENDCVDGSDEEIHLC------------------- -------------------------------------------------- -------------------------------------------CRPGFKP STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQAIDYDWDPEGIG LSVVYYTVLSQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNGDRIYWS DSKEDVIESIKYDGTDRRLIINDAMKPFSLDIFEDQLYWVAKEKGEVWRQ NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP KCKCSSGYSGEYCE------------------------------------ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------/ ----------------------------CGSGNFRCDNGYCIPASWRCDG TRDCLDDTDEIGCPPRSCGSGFFLCPAEGTCIPSSWVCDQDKDCSDGADE QQNC---------------------------------------------- -------------------------------------------------- --------------------DTCGGHQFTCSNGQCINQNWVCDGDDDCQD SGDEDGCESNQRHHTCYPREWACPGSGRCISMDKVCDGVPDCPEGEDE-- -----YCGTGLCSILNCEYQCHQTPYGGECFCPPGHIINSNDSRTCIDFD DCQIWGICDQKCESRQGRHQCLCEEGYILERGQHCKSNDSFSAASIIFSN GRDLLVGDLHGRNFRILAESKNRGIVMGVDFHYQKHRVFWTDPMQAKVFS TDINGLNTQEILNVSIDAPENLAVDWINNKLYLVETRVNRIDVVNLEGNQ RVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKD LVTTKLGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSL VPHPFGISLFEEHVFFTDWTKMAVMKANKFTDTNPQVYHQSSLTPFGVTV YHALRQPNATNPCGNNNGGCAQICVLSHRTDNGGLGYRCKCEFGFELDAD EHHCVAVKNFLLFSSQTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDA QHSTIFYSDLSKNIIYQQKIDGTGKEVITANRLQNVECLSFDWISRNLYW TDGGSKSVTVMKLADKSRRQIISNLNNPRSIVVHPAAGYMFLSDWFRPAK IMRAWSDGSHLMPIVNTSLGWPNGLAIDWSTSRLYWVDAFFDKIEHSNLD GLDRKRLGHVDQMTHPFGLTVFKDNVFLTDWRLGAIIRVRKSDGGDMTVV RRGISSIMHVKAYDADLQTGTNYCSQTTHPNGDCSHFCFPVPNFQRVCGC PYGMKLQRDQMTCEGDPAREPPTQQCGSSSFPCNNGKCVPSIFRCDGVDD CHDNSDEHQCGALNNTCSSSAFTCVHGGQCIPGQWRCDKQNDCLDGSDEQ NCPTRSPSSTCPPTSFTCDNHMCIPKEWVCDTDNDCSDGSDEKNCQASGT CHPTQFRCPDHRCISPLYVCDGDKDCVDGSDEAGCVLNCTSSQFKCADGS SCINSRYRCDGVYDCKDNSDEAGCPTRPPGMCHPDEFQCQGDGTCIPNTW ECDGHPDCIQGSDEHNGCVPKT---------------------------- -------------------------------------------------- NQDSCLHFNGGCTHRCIQGPFGATCVCPIGYQLANDTKTCEDVNECDIPG FCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTASENLLLVVASRDKIIM DNITAHTHNIYSLVQDVSFVVALDFDSVTGRVFWSDLLEGKTWSAFQNGT DKRVVHDSGLSLTEMIAVDWIGRNIYWTDYTLETIEVSKIDGSHRTVLIS KNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIY WPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGQNRRQVIASDLVLHHPHAL TLFEDSVFWTDRGTHQVMQANKWHGRNQSVVMYSVPQPLGIIAIHPSRQP SSPNPCASATCSHLCLLSAQEPRHYSCACPSGWNLSDDSVNCVRGDQPFL ISVRENVIFGISLDPEVKSNDAMVPISGIQHGYDVEFDDSEQFIYWVENP GEIHRVKTDGSNRTAFAPLSLLGSSLGLALDWVSRNIYYTTPASRSIEVL TLRGDTRYGKTLITNDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPA KIASANMDGTSLKILFTGNMEHLEVVTLDIQEQKLYWAVTSRGVIERGNV DGTERMILVHHLAHPWGLVVHGSFLYYSDEQYEVIERVDKSSGSNKVVFR DNIPYLRGLRVYHHRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASG FKLSPDGRSCSPYNSFIVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVL HADVDVANGFIYWCDFSSSVRSSNGIRRIKPNGSNFTNIVTYGIGANGIR GVAVDWVAGNLYFTNAFVYETLIEVIRINTTYRRVLLKVSVDMPRHIVVD PKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAVDHDTGYI YWVDDSLDIIARIHRDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLR KVFQASKQPGNTDPPTVIRDSINLLRDVTIFDEHVQPLSPAELNNNPCLQ SNGGCSHFCFALPELPTPKCGCAFGTLEDDGKNCATSREDFLIYSLNNSL RSLHFDPQDHNLPFQAISVEGMAIALDYDRRNNRIFFTQKLNPIRGQISY VNLYSGASSPTILLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGS NRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNT SLVWPNGLTLDLETDLLYWADASLQKIERSTLTGSNREVVISTAFHSFGL TVYGQYIYWTDFYTKKIYRANKYDGSDLIAMTTRLPTQPSGISTVVKTQQ QQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGSWYLANDNKYCVVDTGA RCNQFQFTCLNGRCISQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTC ANGRCVPYHYRCDFYNDCGDNSDEAGCLF--------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------------------------------CRDDQFTCQNGQCITK LYVCDEDNDCGDGSDEQEHLCHTPEPTCPPHQFRCDNGHCIEMGTVCNHV DDCSDNSDEKGCGINECQDSSISHCDHNCTDTITSFYCSCLPGYKLMSDK RTCVDIDECKETPQLCSQKCENVIGSYICKCAPGYIREPDGKSCRQNSNI EPYLVFSNRYYIRNLTIDGTSYSLILQGLGNVVALDFDRVEERLYWIDAE KQIIERMFLNKTNQETIISHRLRRAESLAVDWVSRKLYWLDAILDCLFVS DLEGRQRKMLAQHCVDANNTFCFENPRGIVLHPQRGYVYWADWGDHAYIA RIGMDGTNKTVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGH HRHTVYDGTLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNT THKPFDIHVLHPYRQPIMSNPCATNNGGCSHLCLIKAGGRGFTCECPDDF QTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDESDL CPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCEAN EWQCANKRCIPEYWQCDSVDDCLDNSDEDPSHCASRTCRPGQFKCNNGRC IPQSWKCDVDNDCGDYSDEPIHECMTAAYNCDNHTEFSCKTNYRCIPQWA VCNGFDDCRDNSDEQGCESVPCHPSGDFRCGNHHCIPLRWKCDGIDDCGD NSDEESCVPRECTESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKT CHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMF ECKNHVCIQSFWICDGENDCVDGSDEEIHLC------------------- -------------------------------------------------- -------------------------------------------CRPGFKP STLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERC AADGSPPLLLLPENVRIRKYNISSEKFSEYLEEEEHIQAIDYDWDPEGIG LSVVYYTVLSQGSQFGAIKRAYLPDFESGSNNPVREVDLGLKYLMQPDGL AVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLG LMFWTDQGKQPKIESAWMNGEHRSVLASANLGWPNGLSIDYLNGDRIYWS DSKEDVIESIKYDGTDRRLIINDAMKPFSLDIFEDQLYWVAKEKGEVWRQ NKFGKGNKEKLLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPG GYSCACPQGSDFVTGSTVECDAASELPITMPSPCRCMHGGSCYFDENDLP KCKCSSGYSGEYCE------------------------------------ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------* >P1;cluster4_2c_now_3875-3998 structureX:cluster4_2c_now_3875-3998::A::B:::: -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------EEIHLCFNVPCESPQRFRCDNSRCI YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFK- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------/ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------EEIHLCFNVPCESPQRFRCDNSRCI YGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCVSQHYVC DNVDDCGDLSDETGCNLGENRTCAEKICEQNCTQLSNGGFICSCRPGFK- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------* >P1;cluster3_2c_now_2773-3039 structureX:cluster3_2c_now_2773-3039::A::B:::: -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------------------EAGCLFRSCNSTTEFTCSNGRCIPLSY VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQF---------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------/ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------------------EAGCLFRSCNSTTEFTCSNGRCIPLSY VCNGINNCHDNDTSDEKNCPPITCQPDFAKCQTTNICVPRAFLCDGDNDC GDGSDENPIYCASHTCRSNEFQCVSPHRCIPSYWFCDGEADCVDSSDEPD TCGHSLNSCSANQFHCDNGRCISSSWVCDGDNDCGDMSDEDQRHHCELQN CSSTEFTCINSRPPNRRCIPQRWVCDGDADCADALDELQNCTMRACSEGE FSCANGRCIRQSFRCDRRNDCGDYSDERGCSYPPCRDDQF---------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------* >P1;cluster2_2c_now_1266-1355 structureX:cluster2_2c_now_1266-1355::A::B:::: -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------------GCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC NQDSCS-------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------/ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ----------------GCVPKTCSPSHFLCDNGNCIYNSWVCDGDNDCRD MSDEKDCPTQPFRCPSSQWQCPGYSICVNLSALCDGIFDCPNGTDESPLC NQDSCS-------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -----------*

3 3

Regarding licensing registration
by Ansania Salam 26 Jul '23

26 Jul '23

I want to install modeller on my device. But couldn’t complete licensing registration. I dont know what glitch is happening right now. Please advise and help regarding this. I have a Bioinformatics workshop tomorrow, so to attend modeller is required to be installed. Please let me know what I need to do.

1 0

Close contacts between protein and ligand
by majort＠biu.ac.il 21 Jul '23

21 Jul '23

Hi I'm modeling protein with ligands (using the "." options in the sequence file). However, in the final models the contacts between protein side chains and ligands are too close (the template and target have differently sized ligands; the template target ligand has a smaller ligand). Is there a way to avoid this, like giving less weight to the homology terms and greater weight to the standard FF terms? Thanks, Dan

2 1

Adding loops to X-Ray
by majort＠biu.ac.il 16 Jun '23

16 Jun '23

Hi, I'm trying to add 3 loops to a crystal structure (loops are missing) without making any changes to the original X-Ray. I base the script on the existing example script 'examples/automodel/loop.py'. My script: ########################################################## from modeller import * from modeller.automodel import * # Load the AutoModel class log.verbose() env = Environ() code = '5uv1' # directories for input atom files env.io.atom_files_directory = ['.'] # Override the regular LoopModel class to select our own loops class MyLoop(LoopModel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # Select gaps for loop modeling return Selection(self.residue_range('157:A', '163:A'), self.residue_range('434:A', '439:A'), self.residue_range('507:A', '517:A')) a = MyLoop(env, inimodel='5uv1_fill.B99990001.pdb', #code+'.pdb', # initial model of the target sequence=code, # code of the target loop_assess_methods=assess.DOPE) # assess loops with DOPE a.loop.starting_model = 1 # First loop model a.loop.ending_model = 4 # Last loop model a.loop.md_level = refine.very_fast # Loop model refinement level a.make() ########################################################## In the inimodel ('5uv1_fill.B99990001.pdb'), the missing residues have been added and simply appear as a straight line and are only connected to one end. When I try do loop modeling using the above script, the loop atoms hardly move and don't reconnect to the other endpoint. How can I model the loops without making any change to the other atoms. Thanks, Dan

2 3

Negative molpdf values
by Isabel Elliott 23 Mar '23

23 Mar '23

Hi, I am generating and refining models using the LoopModel or DOPELoopModel or DOPEHRLoopModel methods. Sometimes I get negative molpdf values for some of my generated models. What does this mean? I thought that the molpdf should be positive. The models with the most negative molpdf correspond to the most negative (i.e the lowest) DOPE scores - are these therefore the best models? Thanks.

2 1

Design of a chmieric protein from two known structures
by dafnikarr＠gmail.com 15 Mar '23

15 Mar '23

Hello , i want to design a chimeric protein by fusion of subdomains of two known proteins. Do you know how should write the relevant scripts? And how to do the alignment? Should i use the multi template approach and use the two proteins as a template? Thank you! Dafni

3 2

MODELLER installation
by Sehrish Batool 28 Feb '23

28 Feb '23

Hello, I hope this email finds you well. I am struggling to download MODELLER application but facing certian security issues. Can you please help me and guide how can I download and install it. I need Modeller to run a workshop in school to show students the advancement in scientific studies. Thank you. J Kind regards:Sehrish Sent from Yahoo Mail on Android

2 1

Modeller is transforming ZN2 atom names to ZN
by Pedro Guillem 27 Feb '23

27 Feb '23

Hello all, I'm using modeller to mutate a single residue in a PDB template that contains ZN atoms. The mutation is taking place correctly, but the resulting PDB is written with the name ZN instead of ZN2, which is in the original template. My ZN is in a different coordination state and I need the name to stay ZN2 in the mutated structure. I have tried setting env.io.heatatm = True, but the outcome is the same. Is there a way to explicitly set modeller to leave the atom names untouched? Thanks in advance for any help. Pedro Here is my code: env = environ() env.io.atom_files_directory = ['.', './atom_files'] env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') env.io.hetatm = True #Prepare Modeller mdl = model(self.env, file=pdb_file) aln = alignment(self.env) aln.append_model(mdl, atom_files=pdb_file, align_codes=pdb_file) chain_id, res_id = mutatnt.split(":") pointmut = f'{res_id}:{chain_id}' new_residue = "A" sel = selection(mdl.residues[pointmut]) sel.mutate(residue_type=self.res1to3[new_residue]) #mutate # Generate the mutated model aln.append_model(mdl, align_codes='mut') mdl.clear_topology() mdl.generate_topology(aln['mut']) mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl2 = model(self.env, file=pdb_file) mdl.res_num_from(mdl2,aln) # Write the mutated structure to a PDB file mdl.write(file=output_file, model_format='PDB')

2 2