- modeller_usage - salilab.org

completing incomplete PDBs
by Christoph Nimptsch 20 Feb '03

20 Feb '03

Hi, assume, I have a PDB file template with some residues missing, e.g. 5 Amino acids at the beginning, 10 in the middle and 2 at the end of the sequence. Now, I use Modeller to complete the template (I align the PDB to its sequence) and use it for homology modelling. Is this a common procedure? What do you think about it? Will the completed template be reliable or should I leave the gaps of the template unfixed in homology modelling? Thanks in advance, Christoph Nimptsch ------------------------------------------ Christoph Nimptsch Apotheker Pharmazeutisches Institut Arbeitskreis Prof. Kovar Universität Tübingen Auf der Morgenstelle 8 D-72076 Tuebingen Tel.: 07071 / 29 73047 Fax.: 07071 / 29 2470 mailto:christoph.nimptsch@uni-tuebingen.de ------------------------------------------

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homology modelling
by Vidya Harini 12 Feb '03

12 Feb '03

Hi, I have the following confusion kindly give me some suggestions... If there are a set of sequences which are 50% identical in sequence and a homology model has been built for one of them, is it possible to use this model in analysing the features of its other related members on the same model. Thanks in advance vvh

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FW: Problems on installation (fwd)
by Andrej Sali 11 Feb '03

11 Feb '03

-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali(a)salilab.org; Web http://salilab.org -----Original Message----- From: Bozidar Yerkovich [mailto:bozidar@salilab.org] Sent: Tuesday, February 11, 2003 6:41 PM To: Andrej Sali Subject: Problems on installation (fwd) ---------- Forwarded message ---------- Date: Tue, 11 Feb 2003 12:00:21 -0000 From: "edward grew (BITS)" <edward.grew(a)bbsrc.ac.uk> To: "'bozidar(a)salilab.org'" <bozidar(a)salilab.org> Subject: Problems on installation I have just installed Modeller6v2 on a Unix system with the path set to i386-absoft. make install seems to work fine but when trying to run modeller using the mod command i get the following error. ? FORTRAN Runtime Error: ? Bad file specification ? OPEN(UNIT=11,... Any advice on how to rectify this problem would be gratefully recieved. thanks very much for your time Edward Grew

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FW: Problems on installation (fwd)
by Andrej Sali 11 Feb '03

11 Feb '03

-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali(a)salilab.org; Web http://salilab.org -----Original Message----- From: Bozidar Yerkovich [mailto:bozidar@salilab.org] Sent: Tuesday, February 11, 2003 6:41 PM To: Andrej Sali Subject: Problems on installation (fwd) ---------- Forwarded message ---------- Date: Tue, 11 Feb 2003 12:00:21 -0000 From: "edward grew (BITS)" <edward.grew(a)bbsrc.ac.uk> To: "'bozidar(a)salilab.org'" <bozidar(a)salilab.org> Subject: Problems on installation I have just installed Modeller6v2 on a Unix system with the path set to i386-absoft. make install seems to work fine but when trying to run modeller using the mod command i get the following error. ? FORTRAN Runtime Error: ? Bad file specification ? OPEN(UNIT=11,... Any advice on how to rectify this problem would be gratefully recieved. thanks very much for your time Edward Grew

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RE: too many helices
by Andrej Sali 06 Feb '03

06 Feb '03

This is probably due to a very large dimension of the whole system (relative to the number of atoms). I suggest you email me your input file so I can narrow down the problem. Best, Andrej -- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali(a)salilab.org; Web http://salilab.org > -----Original Message----- > From: yinja(a)email.uc.edu [mailto:yinja@email.uc.edu] > Sent: Thursday, February 06, 2003 5:28 PM > To: sali(a)salilab.org > Subject: too many helices > > > Hi, Dr. Sali, > i am running a modeller job, in which there are 45 segment to > enforced to form helix. the job log file complained as > folllows: > =============================================================== > TOP_________> 173 132 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', > ADD_RESTRAIN; > TS = 'ON' > > make_re_417_> Restraint type to be calculated: distance > cnctarea_E> Too many cubes. Increase MAXCUBES. kjidim, > maxcubes: 239250 > 50000 =============================================================== > how do i do to by-pass it? two similar jobs have been done > with few number of helices restraints. thanks. > > > Jian Yin > post-doc > university of cincinnati >

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IMPORTANT Announcements!!!
by Bozidar Yerkovich 27 Jan '03

27 Jan '03

Dear all, As some of you already know our group is moving to UCSF in California. Tomorrow morning Jan 28 2003 the move will start and our servers will be powered down. The transition will take couple of weeks. Although we are doing all we can to make modeller_usage list and a web site available during this downtime, please be patient if you experience technical difficulty either posting to the list or with browsing MODELLER web site. Also we are getting near to a release date for MODELLER 7v0. The plan is to have it out by the end of February, but we also ask you for your understanding and patience if our move affects this release date. We are now in alpha phase testing. Another small detail: our web server has been renamed into: salilab.org, so to go the the MODELLER web page you type: http://salilab.org/modeller And at the end, on a more personal note: I am soon leaving Sali group to join Rosetta Inpharmatics, Inc., in Seattle WA. I wanted to tell you that it was my privilege and pleasure to serve you as a 'MODELLER-man', whatever that might be ;-). I will certainly remain active in this area, so if you have any questions or problems feel free to drop me a line. Email is the same: bozidar(a)salilab.org Very best, Bozidar -- Bozidar Yerkovich, PhD Rockefeller University New York, NY, 10021, USA 212-327-7206 bozidar(a)guitar.rockefeller.edu http://guitar.rockefeller.edu/modeller

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Re: Problem with align2d
by Bozidar Yerkovich 22 Jan '03

22 Jan '03

Hi Andrew, The problem is that you don't have defined carboxyl O atoms in the last residue of your PDB, and since you didn't set: READ_TOPOLOGY GENERATE_TOPOLOGY BUILD_MODEL ...which would read in missing atoms from the topology library, and rebuild the model, you got that warning message. It it not a big deal actually. Best, Bozidar > > > > Dear Bozidar > > Thanks for your assistance. Please find attached my I/O files. > > Andrew >> ----- Original Message ----- >> From: Bozidar Yerkovich <mailto:bozidar@salilab.org> >> To: Andrew Kiggundu <mailto:andrew.kiggundu@fabi.up.ac.za> >> Sent: Tuesday, January 21, 2003 4:46 PM >> Subject: Re: Problem with align2d >> >>> >>> Andrew, >>> >>> Can you please send me your I/O tar ball so that I can try to reproduce the >>> error here at mymachine. >>> >>> Thanks, >>> Bozidar >>> >>> >>> >>> Hi Everybody here, >>> >>> I am new to the modelling world and have successfully installed Modeller >>> v6.2 onto windows2000 PC. Got the tutorial to run fine. started modelling my >>> protein. A series of errors I managed to sort out, using the manual, >>> practical article, the FAQ and this list's archive. However, I have had to >>> send in this somewhat simple problem that may have been addressed several >>> times on the list but I have failed to figure out how to get out of it. >>> >>> I am trying first to align two sequences using align2d like so: >>> READ_MODEL FILE = '1eqk.pdb' >>> SEQUENCE_TO_ALI ALIGN_CODES = '1eqkA' >>> READ_ALIGNMENT FILE = 'PapCys.ali', ALIGN_CODES = 'PapCys', ADD_SEQUENCE = >>> ON ALIGN2D >>> WRITE_ALIGNMENT FILE='PapCys-1eqk.ali', ALIGNMENT_FORMAT = 'PIR' >>> WRITE_ALIGNMENT FILE='PapCys-1eqk.pap', ALIGNMENT_FORMAT = 'PAP' >>> >>> Then I get the following error message: >>> >>> iatmcls_286W MODEL atom not classified: ALA:OT1 ALA >>> iatmcls_286W MODEL atom not classified: ALA:OT2 ALA >>> >>> I have checked all lib files and ALA seems well defined, However, I belive >>> there may be a problem in the ieqk.pdb file which have not touched sine >>> downloading from the PDB database. >>> >>> Can anybody help >>> >>> Andrew >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> -- Bozidar Yerkovich, PhD Rockefeller University New York, NY, 10021, USA 212-327-7206 bozidar(a)salilab.org http://salilab.org/modeller

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Re: conformation change
by Eric Feyfant 22 Jan '03

22 Jan '03

Hi zjnjuct; Everything is in Modeller. Look at the COMPARE or SUPERPOSE commands. Good luck; Eric ------------------------------------ Dr Eric Feyfant Computational Chemist Department of Biological Chemistry Wyeth Research 85 Bolton St. Cambridge, MA 02140 tel: +1 617 665 8987 fax: +1 617 665 8993 email: efeyfant(a)wyeth.com >>> zjnjuct <zjnjuct(a)yahoo.com> 01/22/03 01:20AM >>> Dear friends, I have a question regarding to the conformation change of a protein, say protein's conformation at different temperatures, different solvent environments, and the difference between a potein conformation in bulk water solution and the potein conformation on surfaces... As I know, RMSD, is potentially one of the properties to represent that. But how to calculate that? Anyone can provide me the subroutine for calculating this property? Or we may superimpose the two structures to have a comparison. Any other properties? Or software, free package, helpful websites and any other suggestion? Thank you very much for your reply. zjnjuct --------------------------------- Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now

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conformation change
by zjnjuct 21 Jan '03

21 Jan '03

Dear friends, I have a question regarding to the conformation change of a protein, say protein's conformation at different temperatures, different solvent environments, and the difference between a potein conformation in bulk water solution and the potein conformation on surfaces... As I know, RMSD, is potentially one of the properties to represent that. But how to calculate that? Anyone can provide me the subroutine for calculating this property? Or we may superimpose the two structures to have a comparison. Any other properties? Or software, free package, helpful websites and any other suggestion? Thank you very much for your reply. zjnjuct --------------------------------- Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now

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Array too small. Increase MVSPRM
by Cvetan Stojkoski 21 Jan '03

21 Jan '03

I'm trying to read files using the READ_ALIGNMENT command. However, the file cntains 1701 sequences. The error I receive is the following: amaxseq_223E> Array too small. Increase MVSPRM current maximum, current need: 505 1703 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Is there any way to increase MVSPRM ? Thanks in advance.

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