- modeller_usage - salilab.org

making ideal alpha-helix
by Jan Kosinski 12 Jul '13

12 Jul '13

Dear all, I am having a trouble with making an alpha helix example ( http://salilab.org/modeller/wiki/Make%20alpha%20helix) It works fine for shorter helices, but if I increase helix length and do e.g. m.build_sequence('AAAAAAAAAAAAAAAAAA') then the resulting helix is far from perfect, has local distortions and largely is not recognized as helix by DSSP (it shows mixed H and T conformation), and not drawn as helical cartoon in pymol. The situation does not improve if I increase the number of conjugate gradient steps. The extent of distortions does seem to be somewhat sequence dependent. Is there a better way of making an ideal alpha helix with Modeller ? I tested on Modeler 9.11 and 9.12. Thanks in advance for help, Jan

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multiple templates alignment with target
by Ramin Ekhteiari 05 Jul '13

05 Jul '13

Hi, Would you please let me know, by which python script can I align multiple templates with my target? Cheers,

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Preserving orientation of structure
by Thomas Albers 05 Jul '13

05 Jul '13

Hello! I would like to model a poorly resolved loop in a crystal structure on another crystal structure where that loop is better resolved. This is easy to do, however, this loop has coordinates that fit the target structure. Is there a way to tell Modeller to fit the source, so I won't have to reorient that loop after? Thomas

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Re: [modeller_usage] SOLVED headache with alignment
by Francesco Pietra 02 Jul '13

02 Jul '13

That was the procedure that I followed. thanks francesco On Tue, Jul 2, 2013 at 8:41 PM, flavio seixas <oivalf_nix(a)yahoo.com> wrote: > Hi, > It is just a suggestion. > Usualy the pdb file list the protein residues first, followed by the > hetatoms. > Try to edit the pdb file of your template, placing chloride ions coordinates > after the last residue of each protein chain and renumber the chloride > residues to be sequential. > I had a similar problem and it works to me. > Good lucky. > > Flavio > > ________________________________ > From: Francesco Pietra <chiendarret(a)gmail.com> > To: modeller_usage(a)salilab.org > Sent: Tuesday, July 2, 2013 3:06 PM > Subject: [modeller_usage] SOLVED headache with alignment > > I checked that the format I used for hetatm is allowed. However, I > could not obtain the chloride ion at each subunit. Therefore, I went > on with the multimer generated by modeller and placed "manually" the > chloride ions in accordance with the crystal structure. > fp > > > ---------- Forwarded message ---------- > From: Francesco Pietra <chiendarret(a)gmail.com> > Date: Sun, Jun 30, 2013 at 11:51 AM > Subject: Fwd: headache with alignment > To: modeller_usage(a)salilab.org > > > I have further simplified, first using "w" for water and setting true > for w, then removing all water molecules, leaving, as hetatm, only one > chloride ion per chain, with alignment.ali that reads > > >>P1;4FZ0_pure > structureX:4FZ0_pure: 50 :A:+1221:C:::-1.00:-1.00 > ------------------------------------CFMGSLALLALVCTNRIQYYFLYP > HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE > KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG > KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ > DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC > ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK > ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD > IGGQMGLFIGASILTVLELFD---------./----------------------------- > --VVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLNEFRFS > RVTKNDLYHAGELLALLNNRYEIPDTQTADEKQLEILQDKANFRNFKPKPFNMLEFYDRA > GHDIREMLLSCFFRGEQCSPEDFKVVFTRYGKCYTFNAGQDGKPRLITMKGGTGNGLEIM > LDIQQDEYLPVWGETDETSFEAGIKVQIHSQDEPPLIDQLGFGVAPGFQTFVSCQEQRLI > YLPPPWGDCKATTGDSEFYDTYSITACRIDCETRYLVENCNCRMVHMPGDAPYCTPEQYK > ECADPALDFLVEKDNEYCVCEMPCNVTRYGKELSMVKIPSKASAKYLAKKYNKSEQYIGE > NILVLDIFFEALNYETIEQKKAYEVAGLLGDIGGQMGLFIG ASILTVL------------ > -./----------------------------LKRVVWALCFMGSLALLALVCTNRIQYYFL > YPHVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTA > DEKQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTR > YGKCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIH > SQDEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRI > DCETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRY > GKELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLL > GDIGGQMGLFIGASILTVLE------------.* > > >>P1; 4FZ0_pure_fill > sequence::::::::: > GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP > HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE > KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG > KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ > DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC > ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK > ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD > IGGQMGLFIGASILTVLELFDYAYEVIKHR./GQPVSIQAFASSSTLHGISHIFSYERLSL > KRVVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLNEFRFS > RVTKNDLYHAGELLALLNNRYEIPDTQTADEKQLEILQDKANFRNFKPKPFNMLEFYDRA > GHDIREMLLSCFFRGEQCSPEDFKVVFTRYGKCYTFNAGQDGKPRLITMKGGTGNGLEIM > LDIQQDEYLPVWGETDETSFEAGIKVQIHSQDEPPLIDQLGFGVAPGFQTFVSCQEQRLI > YLPPPWGDCKATTGDSEFYDTYSITACRIDCETRYLVENCNCRMVHMPGDAPYCTPEQYK > ECADPALDFLVEKDNEYCVCEMPCNVTRYGKELSMVKIPSKASAKYLAKKYNKSEQYIGE > NILVLDIFFEALNYETIEQKKAYEVAGLLG DIGGQMGLFIGASILTVLELFDYAYEVIKH > R./GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFL > YPHVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTA > DEKQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTR > YGKCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIH > SQDEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRI > DCETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRY > GKELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLL > GDIGGQMGLFIGASILTVLELFDYAYEVIKHR.* > > The error message is that three resids more in the sequence than in > the pdb. It deals of the three chlorides. Is that allowed, as I did, > to set "." for hetatm after "-" for missing amino acids/ It seems to > be incorrect. > > thanks > francesco pietra > > > ---------- Forwarded message ---------- > From: Francesco Pietra <chiendarret(a)gmail.com> > Date: Sun, Jun 30, 2013 at 8:12 AM > Subject: Fwd: headache with alignment > To: modeller_usage(a)salilab.org > > > Removing all dots for heatm, and commenting out "env.io.hetatm = True" > no error messages. Actually, both a chloride ion and water molecules > follow, in that order, the aa on the PDB file. > fp > > > ---------- Forwarded message ---------- > From: Francesco Pietra <chiendarret(a)gmail.com> > Date: Sun, Jun 30, 2013 at 7:28 AM > Subject: Fwd: headache with alignment > To: modeller_usage(a)salilab.org > > > I forgot to mention that the error message of my previous post is > misleading. The F to F matching at chainB F189 is perfect. The cause > why V is seen in place of F should be looked for elsewhere. I retried > by avoiding gaps between the three subunits (see please attachment), > with same error message. > > Thanks for advice > francesco pietra > > > > ---------- Forwarded message ---------- > From: Francesco Pietra <chiendarret(a)gmail.com> > Date: Sat, Jun 29, 2013 at 6:58 PM > Subject: headache with alignment > To: modeller_usage(a)salilab.org > > > Hello: > Could a nice person help correcting the mismatch described by mod9.11 > for missing residues with a trimer? > > read_te_291E> Sequence difference between alignment and pdb : > x (mismatch at alignment position 551) > Alignment .....VVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLNEFR > PDB DFKVVFTRYGKCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEA > Match ***** * > Alignment residue type 18 (V, VAL) does not match pdb > residue type 5 (F, PHE), > for align code XYZ_pure (atom file XYZ_pure), pdb residue number > "189", chain "B" > > > alignment.ali: > >>P1;XYZ0_pure > structureX:XYZ_pure: 50 :A:+1221:C:::-1.00:-1.00 > ------------------------------------CFMGSLALLALVCTNRIQYYFLYP > HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE > KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG > KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ > DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC > ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK > ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD > IGGQMGLFIGASILTVLELFD---------.............................. > ............................................................ > ......................................................./ > -------------------------------VVWALCFMGSLALLALVCTNRIQYYFLYP > HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE > KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG > KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ > DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSE FYDTYSITACRIDC > ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK > ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD > IGGQMGLFIGASILTVL-------------.............................. > ............................................................ > ......................................................./ > ----------------------------LKRVVWALCFMGSLALLALVCTNRIQYYFLYP > HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE > KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG > KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ > DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC > ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK > ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD > IGGQMGLFIGASILTVLE------------.............................. > ............................................................ > ....................................................... > * > > > >>P1; XYZ_pure_fill > sequence::::::::: > GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP > HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE > KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG > KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ > DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC > ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK > ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD > IGGQMGLFIGASILTVLELFDYAYEVIKHR.............................. > ............................................................ > ......................................................./ > GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP > HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE > KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG > KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ > DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWG DCKATTGDSEFYDTYSITACRIDC > ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK > ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD > IGGQMGLFIGASILTVLELFDYAYEVIKHR.............................. > ............................................................ > ......................................................./ > GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP > HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE > KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG > KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ > DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC > ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK > ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD > IGGQMGLFIGASILTVLELFDYAYEVIKHR.............................. > ............................................................ > ............................................... ........ > * > > > As the pasted alignment.ali is misreproduced here, even with plain > text, the file is also attached. Dots stand for chloride ions and > water. > > Thanks a lot > francesco pietra > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >

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SOLVED headache with alignment
by Francesco Pietra 02 Jul '13

02 Jul '13

I checked that the format I used for hetatm is allowed. However, I could not obtain the chloride ion at each subunit. Therefore, I went on with the multimer generated by modeller and placed "manually" the chloride ions in accordance with the crystal structure. fp ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Sun, Jun 30, 2013 at 11:51 AM Subject: Fwd: headache with alignment To: modeller_usage(a)salilab.org I have further simplified, first using "w" for water and setting true for w, then removing all water molecules, leaving, as hetatm, only one chloride ion per chain, with alignment.ali that reads >P1;4FZ0_pure structureX:4FZ0_pure: 50 :A:+1221:C:::-1.00:-1.00 ------------------------------------CFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFD---------./----------------------------- --VVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLNEFRFS RVTKNDLYHAGELLALLNNRYEIPDTQTADEKQLEILQDKANFRNFKPKPFNMLEFYDRA GHDIREMLLSCFFRGEQCSPEDFKVVFTRYGKCYTFNAGQDGKPRLITMKGGTGNGLEIM LDIQQDEYLPVWGETDETSFEAGIKVQIHSQDEPPLIDQLGFGVAPGFQTFVSCQEQRLI YLPPPWGDCKATTGDSEFYDTYSITACRIDCETRYLVENCNCRMVHMPGDAPYCTPEQYK ECADPALDFLVEKDNEYCVCEMPCNVTRYGKELSMVKIPSKASAKYLAKKYNKSEQYIGE NILVLDIFFEALNYETIEQKKAYEVAGLLGDIGGQMGLFIGASILTVL------------ -./----------------------------LKRVVWALCFMGSLALLALVCTNRIQYYFL YPHVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTA DEKQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTR YGKCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIH SQDEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRI DCETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRY GKELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLL GDIGGQMGLFIGASILTVLE------------.* >P1; 4FZ0_pure_fill sequence::::::::: GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFDYAYEVIKHR./GQPVSIQAFASSSTLHGISHIFSYERLSL KRVVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLNEFRFS RVTKNDLYHAGELLALLNNRYEIPDTQTADEKQLEILQDKANFRNFKPKPFNMLEFYDRA GHDIREMLLSCFFRGEQCSPEDFKVVFTRYGKCYTFNAGQDGKPRLITMKGGTGNGLEIM LDIQQDEYLPVWGETDETSFEAGIKVQIHSQDEPPLIDQLGFGVAPGFQTFVSCQEQRLI YLPPPWGDCKATTGDSEFYDTYSITACRIDCETRYLVENCNCRMVHMPGDAPYCTPEQYK ECADPALDFLVEKDNEYCVCEMPCNVTRYGKELSMVKIPSKASAKYLAKKYNKSEQYIGE NILVLDIFFEALNYETIEQKKAYEVAGLLGDIGGQMGLFIGASILTVLELFDYAYEVIKH R./GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFL YPHVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTA DEKQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTR YGKCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIH SQDEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRI DCETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRY GKELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLL GDIGGQMGLFIGASILTVLELFDYAYEVIKHR.* The error message is that three resids more in the sequence than in the pdb. It deals of the three chlorides. Is that allowed, as I did, to set "." for hetatm after "-" for missing amino acids/ It seems to be incorrect. thanks francesco pietra ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Sun, Jun 30, 2013 at 8:12 AM Subject: Fwd: headache with alignment To: modeller_usage(a)salilab.org Removing all dots for heatm, and commenting out "env.io.hetatm = True" no error messages. Actually, both a chloride ion and water molecules follow, in that order, the aa on the PDB file. fp ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Sun, Jun 30, 2013 at 7:28 AM Subject: Fwd: headache with alignment To: modeller_usage(a)salilab.org I forgot to mention that the error message of my previous post is misleading. The F to F matching at chainB F189 is perfect. The cause why V is seen in place of F should be looked for elsewhere. I retried by avoiding gaps between the three subunits (see please attachment), with same error message. Thanks for advice francesco pietra ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Sat, Jun 29, 2013 at 6:58 PM Subject: headache with alignment To: modeller_usage(a)salilab.org Hello: Could a nice person help correcting the mismatch described by mod9.11 for missing residues with a trimer? read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 551) Alignment .....VVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLNEFR PDB DFKVVFTRYGKCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEA Match ***** * Alignment residue type 18 (V, VAL) does not match pdb residue type 5 (F, PHE), for align code XYZ_pure (atom file XYZ_pure), pdb residue number "189", chain "B" alignment.ali: >P1;XYZ0_pure structureX:XYZ_pure: 50 :A:+1221:C:::-1.00:-1.00 ------------------------------------CFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFD---------.............................. ............................................................ ......................................................./ -------------------------------VVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVL-------------.............................. ............................................................ ......................................................./ ----------------------------LKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLE------------.............................. ............................................................ ....................................................... * >P1; XYZ_pure_fill sequence::::::::: GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFDYAYEVIKHR.............................. ............................................................ ......................................................./ GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFDYAYEVIKHR.............................. ............................................................ ......................................................./ GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFDYAYEVIKHR.............................. ............................................................ ....................................................... * As the pasted alignment.ali is misreproduced here, even with plain text, the file is also attached. Dots stand for chloride ions and water. Thanks a lot francesco pietra

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automodel/Mymodel
by Ramin Ekhteiari 01 Jul '13

01 Jul '13

Hi, I want to ask a base question, please let me know the main deference between these two python scripts. I suppose the deference is *this*: the first one do the comparative modeling with the base of template for all residues, but the second one, do the same except for residues 197 - 198. But I see a main deference between the results (output structures) are the applied methods of these two script are the same or not? Cheers Ramin #1 env = environ() a = automodel(env, alnfile='Drd2-3SN6.ali', knowns='3SN6', sequence='Drd2', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1000 a.ending_model = 1000 a.make() ----------------------------------------------------------------------------------------- #2 class MyModel(automodel): def select_atoms(self): return selection(self) - selection(self.residue_range('197', '198')) env = environ() a = MyModel(env, alnfile = 'Drd2-3SN6.ali', knowns = '3SN6', sequence = 'Drd2', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model= 1005 a.ending_model = 1005 a.make() ---------------------------------------------------------

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headache with alignment
by Francesco Pietra 30 Jun '13

30 Jun '13

Hello: Could a nice person help correcting the mismatch described by mod9.11 for missing residues with a trimer? read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 551) Alignment .....VVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLNEFR PDB DFKVVFTRYGKCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEA Match ***** * Alignment residue type 18 (V, VAL) does not match pdb residue type 5 (F, PHE), for align code XYZ_pure (atom file XYZ_pure), pdb residue number "189", chain "B" alignment.ali: >P1;XYZ0_pure structureX:XYZ_pure: 50 :A:+1221:C:::-1.00:-1.00 ------------------------------------CFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFD---------.............................. ............................................................ ......................................................./ -------------------------------VVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVL-------------.............................. ............................................................ ......................................................./ ----------------------------LKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLE------------.............................. ............................................................ ....................................................... * >P1; XYZ_pure_fill sequence::::::::: GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFDYAYEVIKHR.............................. ............................................................ ......................................................./ GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFDYAYEVIKHR.............................. ............................................................ ......................................................./ GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFDYAYEVIKHR.............................. ............................................................ ....................................................... * As the pasted alignment.ali is misreproduced here, even with plain text, the file is also attached. Dots stand for chloride ions and water. Thanks a lot francesco pietra

1 3

Denovo loop remodeling
by Ramin Ekhteiari 28 Jun '13

28 Jun '13

Hi, Is there any Denovo loop remodeling on the base of the fragment data base in MODELLER? Cheers, Berk

2 3

Long loop omitting
by Ramin Ekhteiari 25 Jun '13

25 Jun '13

Hi, I am predicting a protein by homology method, this protein has a long loop (i.e., 40 resides) and there is no any residues in template for modeling, I don't want modeler to model this loop site by energy minimizing method and leave it. So how can I arrange this in build script. Cheers, Ramin

2 1

Model of the GFP
by James Starlight 25 Jun '13

25 Jun '13

Dear Modeller Users! I've forced with the problem during preparation of the model of my Green Fluorescent protein. In particular this model consist of heteroatomic chromophore group which is the part of the protein polypeptide chain. Because my initial pdb file have missed N term (first 1-10 residues) I'd like to build full-residue model including chromophore group which present in the pdb file as the HETATM. below you can see my alignment file as well as script >P1;input structureX:input:6: ::225 : ::-1.00:-1.00 -----NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQ.SKVYVKHPADIP DYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGE IHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL* >P1;seq sequence:seq: : : : ::: 0.00: 0.00 MRSSKNVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQ.SKVYVKHPADIP DYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGE IHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL* # Homology modeling with multiple templates from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # Read in HETATM records from template PDBs env.io.hetatm = True # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] allow_alternates=True a = automodel(env, alnfile = 'align-multiple_new.ali', # alignment filename knowns = 'input', # codes of the templates sequence = 'seq') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 30 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling Here in both sequences dot (.) in the SPQ.SK motif correspond to the chromophore group (env.io.hetatm = True). Unfortunatelly I have error after processing this _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence not found in PDB file: 1 ./input.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q). How I could fix it ? Thanks for help, James

2 3