December 2003 - modeller_usage

Modeller input alignment file
by christos Kouriniadis 26 Jan '04

26 Jan '04

Hello everybody, I am doing a project on comparative modelling, by using modeller. My problem is the following: I am trying to make an input file with PDB structures aligned in PIR format. However, when I am reading the modeller manual, I see that the worked example is in the form: P1;2ald structureX:2ald:2:@:363:@:aldolase:human muscle:2.00:0.17 * If you go to the section "display/download file", in the PDB website, you will get the usual big file. But when I have a look at this file, I see that ATOM has three coordinates: -20.521 45.890 70.464 How from these coordinates I get the :2:@:363:@: ??? Is there a formula that transforms it? I would be grateful if you could give me a hint on this. Thanks, Christos Kouriniadis _________________________________________________________________ Add photos to your e-mail with MSN 8. Get 2 months FREE*. http://join.msn.com/?page=features/featuredemail

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help!
by nick jones 05 Jan '04

05 Jan '04

I have a problem with modeller. I am new to the program and I couldnt find a manual for modeller usage in a command prompt. If anyone has a manual for modeller usage in MS-DOS command prompt or knows how to open pdb files from it please help! --------------------------------- Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing

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Gaps in pdb file
by MacFarlane, Amanda J. 22 Dec '03

22 Dec '03

Dear Modellers, I'm relatively new to Modeller, and I have a question which I hope has an easy answer. Whenever the pdb file for a solved structure has a gap in the residue numbers (so, for instance, it jumps from residue 300 to 315), I get an error saying that the number of residues in the alignment file and the pdb file are different. How can I fix this problem? Thanks! Amanda MacFarlane Amanda MacFarlane Autoimmune Disease Group/Diabetes Ottawa Health Research Institute Lab N1 Box 221 501 Smyth Road Ottawa ON K1S 5B7

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About rotamers ?
by Mickael Krzeminski 18 Dec '03

18 Dec '03

Hi! I have never read something about rotamers... I would like to know wether MODELLER6v2 cares about rotamers ? And if yes, what method (I should say 'library') is used in this case ? Best resgards, Mickaël

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simple question
by Michael Grabe 15 Dec '03

15 Dec '03

dear modellers, I want to make a 3 A harmonic distance restraint between these two atoms: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ATOM 464 CD GLU 56 -7.029 6.474 8.483 1.00130.43 1SG 465 ...... ATOM 545 CZ ARG 66 -13.040 -0.756 16.131 1.00255.28 1SG 546 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% But for the life of me, I can't get the syntax right inside the special_restraints subroutine. Can someone help me out? -Michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. Post-doctoral Fellow Howard Hughes Medical Institute University of California, San Francisco 533 Parnassus Ave. San Francisco, CA 94143 mgrabe(a)itsa.ucsf.edu tel: ++ 415.476.6585 http://itsa.ucsf.edu/~mgrabe

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Max templates
by Jenny.Carmichael＠csiro.au 14 Dec '03

14 Dec '03

Dear modellers, Just a quick question, is there a maximum number of templates that it is possible to use, say 40, 50 or 60 for example, derived from NMR structure files. JennyC

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online interface
by rathankar rao 04 Dec '03

04 Dec '03

hi 1. are there any commands to check the intermolecular contacts incase of a macromolecule.plz explain. if webinterface is present plz give the URL 2. DOES Modeller has online interface N.Rathankar Assistant Proffessor in physics Madanapalle Institute of Technological Sciences (MITS). INDIA WEBSITE: http://www.geocities.com/rathankar/ --------------------------------- Do you Yahoo!? Free Pop-Up Blocker - Get it now

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Re: [modeller_usage] Upper limit distance restraint
by Thorsten Schweikardt 04 Dec '03

04 Dec '03

Hello Miha, you have to include a user distance-restraint, the concerning chapter in the manual about these restraints and the parameters used is named "2.5 Calculation of spatial restraints". There is also the FAQ at http://salilab.org/modeller/FAQ.html, open it and look for "I want to add my own restraints". This is an example (to be inserted in your .top file): ... [rest of your .top-file...] CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS = 'CA:25' 'CA:187' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 10.0 1.0 SET ADD_RESTRAINTS = off RETURN END_SUBROUTINE I hope this helps you getting started. Best wishes and happy modelling, Thorsten Schweikardt Molecular Biophysics Mainz, Germany > > -----Ursprüngliche Nachricht----- > > Von: Miha Pavsic [mailto:miha.pavsic@ijs.si] > > Gesendet: Mittwoch, 3. Dezember 2003 10:54 > > An: modeller_usage(a)salilab.org > > Betreff: [modeller_usage] Upper limit distance restraint > > > > > > Hello Modeller users, > > > > I am looking for a way to specify upper limit distance restraint > > between CA atoms of two residues (eg., max 10 A between CA:25 and > > CA:187). Can someone please give me an example of doing this? > > > > Regards, > > Miha Pavsic > > >

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RE: [modeller_usage] GTP RTF
by Eswar Narayanan 03 Dec '03

03 Dec '03

It's a modified version of CHARMM-22 for the topology libraries. Eswar. --- Eswar Narayanan, Ph.D Mission Bay Genentech Hall 600 16th Street, Suite N474Q University of California, San Francisco San Francisco, CA 94143-2240 (CA 94158 for courier) Tel +1 (415) 514-4233; Fax +1 (415) 514-4231 http://www.salilab.org/~eashwar > -----Original Message----- > From: devary(a)jct.ac.il [mailto:devary@jct.ac.il] > Sent: Wednesday, December 03, 2003 10:28 AM > To: Eswar Narayanan > Subject: RE: [modeller_usage] GTP RTF > > thank you for the help please tell me which version of charmm > modeller is using > yoram > > > Quoting Eswar Narayanan <eashwar(a)salilab.org>: > > > Please check $MODINSTALLXvX/modlib/top_heav.lib. > > > > Best > > Eswar. > > > > --- > > Eswar Narayanan, Ph.D > > Mission Bay Genentech Hall > > 600 16th Street, Suite N474Q > > University of California, San Francisco > > San Francisco, CA 94143-2240 (CA 94158 for courier) > > Tel +1 (415) 514-4233; Fax +1 (415) 514-4231 > > http://www.salilab.org/~eashwar > > > > > -----Original Message----- > > > From: modeller_usage-bounces(a)salilab.org [mailto:modeller_usage- > > > bounces(a)salilab.org] On Behalf Of devary(a)jct.ac.il > > > Sent: Wednesday, December 03, 2003 12:26 AM > > > To: modeller_usage(a)salilab.org > > > Subject: [modeller_usage] GTP RTF > > > > > > Dear Sir I am trying to build a model with GTP can you pls > > > tell were can I find parameters for GTP or you have it somewhere > > > yoram > > > > > > _______________________________________________ > > > modeller_usage mailing list > > > modeller_usage(a)salilab.org > > > http://salilab.org/mailman/listinfo/modeller_usage > > > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage(a)salilab.org > > http://salilab.org/mailman/listinfo/modeller_usage > >

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GTP RTF
by devary＠jct.ac.il 03 Dec '03

03 Dec '03

Dear Sir I am trying to build a model with GTP can you pls tell were can I find parameters for GTP or you have it somewhere yoram

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