- modeller_usage - salilab.org

Modeling loop from a part of a sequence
by Robert Selwyne 08 Sep '09

08 Sep '09

Dear Modeller Users Loop residues from 1223 to 1245 are missing in PDB:2RFN (target). I want to construct this missing part by taking loop residues 382 to 406 from PDB:3LCK (template). Could you please tell me how to model this? Regards Robert

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validation
by Adriana Esteves 07 Sep '09

07 Sep '09

Dear all: I am new in this task of homology modeling and I want to know how can I validate my model. I heard about several programs on line like ANOLEA, Verify 3D and What_check. Any one knows about the utility of this programs? Thank you very much Adriana

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Including hetatm when hetatm does not immediately follow ATOM list
by Shuo Huai Johnny Wu 04 Sep '09

04 Sep '09

Hi I am trying to thread a target rhodopsin sequence from humans to the template bovine rhodopsin structure (pdb1f88). The rhodopsin crystal structure exists in the pdb file as a crystal dimer represented by chain A and B. Each chain is 348 amino acids, but there are missing residues on both chains. I used the simple automodel script, and it worked well. When I tried to include both the ligands and the carbohydrates (hetatms) into the structure by setting env.io.hetatm = True, I get errors that do not make much sense to me. My structure pdb is different from the hetatm example pdb for in that the ligands hetatm residue numbers do not immediately follow the atom residue sequence. Here is a summary of the heteroatoms that follow the seqres HET NAG A 501 14 HET NAG A 502 14 HET NAG B 601 14 HET NAG B 602 14 HET MAN B 603 11 HET NAG A 701 14 HET NAG A 702 14 HET NAG B 801 14 HET NAG B 802 14 HET HG A 901 1 HET HG B 902 1 HET HG A 903 1 HET HG B 904 1 HET HG A 905 1 HET HG B 906 1 HET ZN A 907 1 HET ZN B 908 1 HET ZN B 909 1 HET ZN A 910 1 HET RET A 977 20 HET RET B 978 20 There are no amino acids residue numbers that flank the hetam numbers. That is, there is no amino acid numbers from 803 to 900. These entries are left unspecified. All hetatms are described after chain B in the ATOM section. ATOM 5067 OD1 ASN B 326 30.599 31.795 -7.049 1.00107.30 O ATOM 5068 ND2 ASN B 326 30.914 33.473 -8.519 1.00107.62 N TER 5069 ASN B 326 HETATM 5070 C1 NAG A 501 37.620 3.757 -28.808 1.00 65.21 C HETATM 5071 C2 NAG A 501 38.420 5.021 -29.058 1.00 65.24 C HETATM 5072 C3 NAG A 501 37.477 6.163 -29.455 1.00 66.66 C I first tried to include all hetatms as '.' with the unspecified residues past the end of the protein (aa 348) replaced with '-'. >P1;B._taurus structureY:B._taurus:1 :A: 977:A:ground state rhodopsin:Bovine: : MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLA VADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFT WVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAA----S ATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTT LCCGKNP------STTVSKTETSQVAPA---------------------------------------------------- -------------------------------------------------------------------------------- --------------------..---------------------------------------------------------- -------------------------------------------------------------------------------- ------------------------------------------------------------..------------------ -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- --------------------.-.-.----.-------------------------------------------------- ----------------.* It results in this error: _modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 347 650 For alignment entry: 1 B._taurus When I forgo the trailing '-' and simply append hetatms to the end in a series of '.': >P1;B._taurus structureY:B._taurus:1 :A: 977:A:ground state rhodopsin:Bovine: : MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAA----SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNP------STTVSKTETSQVAPA........* I get the following error: _modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 347 650 For alignment entry: 1 B._taurus I've seen the following thread and tried to follow the advice enclosed, but I am still having trouble. http://salilab.org/archives/modeller_usage/2008/msg00183.html http://salilab.org/archives/modeller_usage/2008/msg00186.html The structure ID of bovine rhodopsin is pdb1f88. Thanks in advance, -- Shuo Huai Johnny Wu -- Shuo Huai Johnny Wu

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validation
by Adriana Esteves 02 Sep '09

02 Sep '09

Dear all: I am new in this task of homology modeling and I want to know how can I validate my model. I heard about several programs on line like ANOLEA, Verify 3D and What_check. Any one knows about the utility of this programs? Thank you very much Adriana

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Issues Installing Modeller Ubuntu 8.10
by Ocar Campos 01 Sep '09

01 Sep '09

Hello: I have some issues installing modeller 9v7 in my linux distribution, I have a 32 bits machine, and already have installed all the libraries for the modeller to run, which would be python 2.5.2, glib package, wich my sinaptics shows version 2.8, and gcc, c++ and fortran. I installed from the .rpm package, following the instruction on the web, so far, all it's ok, but when running something like mod9v7 build_profile.py I get the following message: Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback I have already set home path, that would be: PYTHONHOME=/usr/bin/python. I also looked for some info about the issue and I got to this: http://salilab.org/archives/modeller_usage/2007/msg00126.html. Followed the instructions there but when building with python got another issue: root@XXXXXX:/usr/lib/modeller9v7/src/swig# python setup.py build Traceback (most recent call last): File "setup.py", line 20, in <module> glib['include_dirs'], KeyError: 'include_dirs' So I don't get any file to replace if it is something python related, anyone knows any solution to this? or what I am doing wrong? Cheers. O'car Campos C. Bioinformatics Engineering Student. University of Talca. Chile.

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validation
by Adriana Esteves 31 Aug '09

31 Aug '09

Dear all: I am new in this task of homology modeling and I want to know how can I validate my model. I heard about several programs on line like ANOLEA, Verify 3D and What_check. Any one knows about the utility of this programs? Thank you very much Adriana

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MODELLER behaviour with non-standard residues / HETATM
by Thomas Juettemann 29 Aug '09

29 Aug '09

Dear all, could someone enlighten me how MODELLER treats non-standard residues. I am using Dunbrack's S2C as a source for ATOM sequences. In the PDB file 1M2W, I have several selenomethionine (MSE) residues, marked as HETATM. Running MODELLER, it seems to convert them to methionine (which I appreciate) and successfully produces a model. My question is: How does MODELLER check / replace HETATM that have a residue identifier that is in the permitted range (not 'X', '.' or '-')? I did not not set env.io.hetatm to true. My apologies if I missed this information in the manual or my question is not clear enough. Many thanks, Thomas Template: http://www.pdb.org/pdb/files/1M2W.pdb (e.g. residue 1,50 & 105) Alignment >P1;1M2W structureX:1M2W:FIRST:@ END:::::: MKLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTLKHLLKKP / MKLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTLKHLLKKP * >P1;P09424-P77260 sequence:P09424-P77260:::::::: MK---------------------ALHFGAGNIGRG----FIGKLL-ADAGIQLTFADV-----NQVVLDALNAR-HSYQVHVVGETEQ-----VDTVSGVNAVSSIGDDVVDLIAQ-----VDLVTTAVGPVV----------LERIAPAIAK------------GQVKRKEQGNESPLNIIACENMVR-GTTQLKGHVMNALPEDAK--AWVEEHVGFVDSAVDRIVPPSASA----------TNDPLEVTVETFSEWIVDKTQFKG--ALPNIPGMELTDNLMAFVERKLFTLNTGHAITAYLGKLAGHQTIRDAILDEKIRAVVKGAME-ESGAVLIKRYGFDADKHAAYIQKILGRFENPYLKDDVERV---GRQPLRKLSAG--DRLIKP-----------------LLGTLEYGL------PHKNLIEGIAAAMHFRSEDDPQAQELAALIADKGPQ--AALAQISGLDANSEVVSEAVTAYKAMQ / ---NLLSAKATLPVYDLNNLAPRIVHLGFGAFHRAHQGVYAD-ILATEHFSDWGYYEVNLIGGEQQI-ADLQQQDNLYTVAEMS-ADVWTARVVGVVKKALHVQIDGLETVLAAMCEPQIAIVSLTITEKGYFHSPATGQLMLDHPMVAADVQNPHQPKTATGVIVEALARRKAAGLPAFTVMSCDNMPENGHVMRDVVTSYAQAVDVKLAQWIEDNVTFPSTMVDRIVPAVTEDTLAKIEQLTGVRDPAGVACEPFRQWVIEDNFVAGRPEWEKAGAELVSDVLPYEEMKLRMLNGSHSFLAYLGYLAGYQHINDCMEDEHYRYAAYGLMLQEQAPTL-KVQGVDLQDYANRLIARYSNPALRHRTWQIAMDGSQKLPQRMLDSVRWHLAHDSKFDLLALGVAGWMRYVGGVDEQGNPIEISDPLLPVIQKAVQSSAEGKARVQSLLAIKAIFGDDLPDNSLFTARVTETYLSLLAHGAKATVAKYSVK--

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database with PIR format, help
by Quiliano Mesa, Miguel Angel 27 Aug '09

27 Aug '09

Dear followers of Modeller I am a new user and I found me with a easy but tedious problem (doing it by hand). I have several sequences in FASTA format so I would like to do the same process such as the basic tutorial with the database "95.pir", my question is... how to convert to PIR format.. should I use a program for this? there is a program for this? anyone have a scritp? I would very grateful if someone can hel me. thanks in advance. Miguel Quiliano.

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remove short helices
by Shawna Frazier 22 Aug '09

22 Aug '09

Hi, When I view my structural model as a cartoon, it contains several short 'helices', composed of only three residues each. The template pdb shows each of these regions as unstructured loops. Therefore, I would like to remove these short helices from my model. Is there a simple way to remove secondary structure? Note, I have tried loop refinement; it worked on a couple of my short helices, but has failed to fix my last one. Any suggestions are appreciated. Thanks.

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Re: [modeller_usage] modeller_usage Digest, Vol 8, Issue 60
by carlos Prudencio 19 Aug '09

19 Aug '09

Hi, I need to do a de novo 3D model because I was't able to find any similar structural to compare. thanks, Carlos R. Prudencio MSN: crprudencio(a)hotmail.com Fone: +34645465174 (Spain) On Aug 19, 2009, at 1:53 AM, modeller_usage-request(a)salilab.org wrote: > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Re: how to evaluate which is the best model in "multiple > template" example (Modeller Caretaker) > 2. Heme in P450 (Storbeck, K, Dr <storbeck(a)sun.ac.za>) > 3. Re: Heme in P450 (Modeller Caretaker) > 4. remove short helices (Shawna Frazier) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 06 Aug 2009 08:50:51 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: albumns <albumns(a)yeah.net> > Cc: modeller_usage <modeller_usage(a)salilab.org> > Subject: Re: [modeller_usage] how to evaluate which is the best model > in "multiple template" example > Message-ID: <4A7AFBDB.3040400(a)salilab.org> > Content-Type: text/plain; charset=UTF-8; format=flowed > > albumns wrote: >> how to evaluate which is the best model in "multiple template" >> example? In the tutorial, it just use the model number 1 for the >> final one. How to judge these models which is better than the left? > > You can evaluate the model quality with the DOPE score (the model with > the lowest DOPE score is most likely to be the best) in the same way > as > the single template example. It doesn't matter how many templates were > used to build the model - the evaluation is of the model itself, not > the > alignment. > >> my another question is that how can we draw the "basic model" and >> multiple templates in the same diagram with GUNplot? > > If you're referring to the plot of DOPE score profiles, shown at the > end > of the basic tutorial, such a plot is only qualitative at best. You > can > only plot a single profile in GNUPLOT, because with multiple > profiles you have to account for the gaps. This is done by the > plot_profiles script in the basic tutorial. To plot multiple > templates, > it should be straightforward to modify that script, adding extra calls > to get_profile() and pylab.plot(). > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 2 > Date: Tue, 18 Aug 2009 19:45:27 +0200 > From: "Storbeck, K, Dr <storbeck(a)sun.ac.za>" <storbeck(a)sun.ac.za> > To: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> > Subject: [modeller_usage] Heme in P450 > Message-ID: > <D698F2F3BBE7504AA43E6B2A7CFFD82D127FA65B14(a)STBEVS06.stb.sun.ac.za> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I am modeling a cytochrome P450, I am able to include the heme in my > model. However, in the templates the heme iron is bound to a cys > residue, but I loose this bond in the model. How can I go about > keeping it in my model? > > Thanks > Karl > > > ------------------------------ > > Message: 3 > Date: Tue, 18 Aug 2009 13:06:24 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: "Storbeck, K, Dr <storbeck(a)sun.ac.za>" <storbeck(a)sun.ac.za> > Cc: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> > Subject: Re: [modeller_usage] Heme in P450 > Message-ID: <4A8B09C0.5030203(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Storbeck, K, Dr <storbeck(a)sun.ac.za> wrote: >> I am modeling a cytochrome P450, I am able to include the heme in my >> model. However, in the templates the heme iron is bound to a cys >> residue, but I loose this bond in the model. How can I go about >> keeping it in my model? > > If you have a CYS residue in your model aligned with that template > residue, then Modeller should automatically keep that bond in your > model > (see the third bullet point at > http://salilab.org/modeller/9v7/manual/node65.html) This does, > however, > require Modeller 9v5 or later. The heuristic is a simple one though > - if > the bond is longer than 2.3A you could just add a simple distance > restraint to approximate this interaction. But really to do this > properly you need to tell Modeller that that CYS residue is not > really a > 'CYS' but is a modified residue (i.e. that it has a bond to your > iron). > For that you'd need to patch your topology using the model.patch() > command and some knowledge of how CHARMM patches work, which can be > gleaned from the CHARMM manual. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 4 > Date: Tue, 18 Aug 2009 16:38:21 -0700 > From: Shawna Frazier <sfrazier(a)caltech.edu> > To: modeller_usage(a)salilab.org > Subject: [modeller_usage] remove short helices > Message-ID: <06A265F6-2F41-4968-86C3-C51B21041AA7(a)caltech.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi, > > When I view my structural model as a cartoon, it contains several > short 'helices', composed of only three residues each. The template > pdb shows each of these regions as unstructured loops. Therefore, I > would like to remove these short helices from my model. Is there a > simple way to remove secondary structure? > > Note, I have tried loop refinement; it worked on a couple of my short > helices, but has failed to fix my last one. > > Any suggestions are appreciated. > Thanks. > > > ------------------------------ > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 8, Issue 60 > *********************************************

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