- modeller_usage - salilab.org

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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Upper limit distance restraint
by Miha Pavsic 03 Dec '03

03 Dec '03

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 *** Miha Pavsic, PhD Student Josef Stefan Institute Dept. of Biochemistry and Molecular Biology Jamova 39, SI-1000 Ljubljana, Slovenia

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problem in installing
by rathankar rao 02 Dec '03

02 Dec '03

hi i have installed modeller6v2 in c:/ in windows68se OS, i also recieved my license key from the author but on entering the license key to modenv.bat and mod.bat, it says wrong license the license provided to me is ****. i dont know how to go with it plz advice 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] malign3d will not align multiple structures
by Mark Daniels 01 Dec '03

01 Dec '03

Hello Oliver- Thank you for the reply. MALIGN3D does not require an alignment file if the structural models have a 1:1 sequence correspondence. In my case I am aligning five models of the same protein. I figured out what the problem was by looking at the .top files in the examples/tutorial-model folder of modeller6v2. As it turns out, I have to add the command SET ALIGN_CODES = 'atip' 'atip' 'atip' 'atip' 'atip' with which MALIGN3D properly loads the five model atip.Bxxx files. The Sanchez and Sali Methods in Molecular Biology article does not mention this (and neither does the manual). Regards- Mark J Daniels markjd(a)scripps.edu Department of Cell Biology The Scripps Research Institute La Jolla, CA On Mon, 1 Dec 2003, Oliver Hucke wrote: > Hi Mark, > > I miss the specification of the alignment file in your top script. I > suppose modeller needs an initial alignment - at least that's how I use > MALIGN3D. The atom files are specified in the alignment file, not in the > script. Please have a look at the example given in the section on > MALIGN3D in the manual. This works fine for me. The initial alignment > can be obtained with the commands SEQUENCE_TO_ALI and MALIGN. > > Hope this helps, > Oliver > > Mark Daniels wrote: > > Hello all- > > > > I'm trying to run malign3d to align multiple models but the routine > > only 'sees' the first structure and does nothing. I'm using the > > malign3d.top file format described in the Sanchez and Sali 2000 Methods > > in Molecular Biology article: > > > > SET OUTPUT_CONTROL = 1 1 1 1 2 > > SET MAXRES = 700 > > SET ATOM_FILES = 'atip.B99990001' 'atip.B99990002' ; > > 'atip.B99990003' 'atip.B99990004' 'atip.B99990005' > > SET WRITE_FIT = on > > MALIGN3D > > > > All the atip.Bxxxx files contain a reasonable structure. Running the > > malign3d.top routine shown above fails to produce any .fit files and > > shows the following error: > > > > openf5__224_> Open 11 OLD SEQUENTIAL atip.B99990001 > > malign3_327W> Only one structure; nothing done. > > > > Would anyone be able to advise me on what I'm missing here or doing wrong? > > > > Thanks in advance- > > > > Mark Daniels > > The Scripps Research Institute > > > > > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage(a)salilab.org > > http://salilab.org/mailman/listinfo/modeller_usage > > > -- > _______________________________________________________________ > > Oliver Hucke, Dr. > Health Sciences Building - K418C > University of Washington 1959 NE Pacific St. > Dept. of Biochemistry phone: (206) 685 7046 > Box 357742 fax : (206) 685 7002 > Seattle, WA 98195-7742 email: ohucke(a)u.washington.edu > _______________________________________________________________ > > >

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