January 2003 - modeller_usage

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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Problem with align2d
by Andrew Kiggundu 20 Jan '03

20 Jan '03

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

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none restraints made
by alarcon＠lncc.br 16 Jan '03

16 Jan '03

Hi all I ran a very simpleton modelling procedure with mod6v2 and got this log file with none restraints made. The procedure spontaneously is aborted. The same procedure runs well when no HETATM are considered. Any hint will be helpful. rgds Frank Alarcon www.brgene.lncc.br ----------------------------------------------------------------------------- TOP FILE : ----------------------------------------------------------------------------- INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'serino_ed1.ali' SET KNOWNS = '1BH6' '1GCI' '1LW6' '1MEE' '1SCJ' '1SUP' '1THM' SET SEQUENCE = 'oooo' SET ATOM_FILES_DIRECTORY = './:../atom_files' SET STARTING_MODEL= 1 SET ENDING_MODEL = 5 SET HETATM_IO = on CALL ROUTINE = 'model' ------------------------------------------------------------------------- THE LOG FILE (ending...) ------------------------------------------------------------------------- Number of atoms to choose from, total : 3220 3220 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : HET Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 439 1: 439: selatm__462_> Number of selected atoms : 13 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 438 : BLK --- 439 : BLK 2 TOP_________> 191 169 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 28880029 28203.152 27.542 make_re_417_> Restraint type to be calculated: distance r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 and the same goes on... ------------------------------------------------- WEBMAIL-LNCC Esta mensagem foi enviada utilizanto IMP.

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bond_length_violation/bond_error
by Ralf Schmid 13 Jan '03

13 Jan '03

Dear all, I'm modelling a protein with some additional NMR-restraints for hydrogens. It does work fine for about half of the models, for the other half I get very high scores in the MODELLER OBJECTIVE FUNCTION. This is due to violations of the bond length potential caused by wrong connections between Ns and Hs of an ARG residue (see logfile below), for the models with the 'good' scores the connections are OK. Any ideas what might mess up the N-H bonds? thanks in advance, ralf logfile: <snip> ------------------------------------------------------------------------ Feature 1 : Bond length potential List of the RVIOL violations larger than : 4.5000 #ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 774 53R 53R NH1 HH11 772 773 3.27 1.00 2.27 89.01 1.00 2.27 89.01 2 775 53R 53R NH1 HH12 772 774 2.57 1.00 1.57 61.57 1.00 1.57 61.57 3 776 53R 53R NH2 HH21 775 776 2.57 1.00 1.57 61.51 1.00 1.57 61.57 4 777 53R 53R NH2 HH22 775 777 3.27 1.00 2.27 89.02 1.00 2.27 89.02 ------------------------------------------------------------------------ <snip> ======================================= Dr. Ralf Schmid Institute of Cell and Molecular Biology The University of Edinburgh King's Buildings Michael Swann Building 3.14 Edinburgh EH9 3JR

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Many templates/targets
by Cvetan Stojkoski 09 Jan '03

09 Jan '03

Hey Modeller users, I'm trying to model 400+ proteins based on ~100 templates. I have an alignmentfile of 1500+ sequences comprising of the templates, targets and others. ClustalW was used to align the sequences. I have a few problems. - The sequences in the alignment file do not match the aminoacids present in the pdb files. _Generally_ the pdb files contain more residues than specified in the aligned sequence. Therefore I have to either concatonate the pdb files or specify the residues in the appropriate residues in the alignment file. - The ID codes in the alignment file do not match the atom file names. - There is no "second" line in each entry in the alignment file. Although all this can be done manually, I can't help but wonder if there is a way to automate/expidate the process. A paper published by Sanhez and Sali (1998) mentioned perl script that allowed for rapid progress through the various steps involved with modelling. Suggestions will be most appreciated. Some of the pdb files are complexes. If it can be avoided I'd prefer not to use these structures . However if I do decide to use some of them, I plan to minimise the E via MD (cns) of the protein (minus the ligand) before using it as a template. What are people's thoughts about this? Many thanks

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How to change a pdb file's chain id without renumbering the residues using Modeller?
by Kong Lesheng 07 Jan '03

07 Jan '03

Hi, I have successed done this under Modeller 4. But under Modeller 6v2, the old script doesn't work. My top file is as follow: READ_MODEL FILE = 'xenl.pdb' RENAME_SEGMENTS SEGMENT_IDS = 'X', RENUMBER_RESIDUES = off WRITE_MODEL FILE = 'xenl.mol', HETATM_IO = on The log file reported that assgn___547E> Incorrect element type for variable: RENUMBER_RESIDUES Element, element type: OFF 4 Command line: RENAME_SEGMENTS SEGMENT_IDS = 'X', RENUMBER_RESIDUES = OFF assgn___525E> Error in TOP variable assignment. compile_563E> Please correct the errors reported above and rerun MODELLER. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I have checked the libary file top.ini in modeller4 and modeller6v2 about RENUMBER_RESIDUES. Under modeller4 , 64 LOGICAL RENUMBER_RESIDUES 1 on # whether to renumber residues from 1 to N Under modeller6v2, 41 INTEGER RENUMBER_RESIDUES 0 # starting residue index for renumbering residues Is it possible to change a pdb file's chain id without renumbering the residues ? Thank you very much! With best regards, Lesheng

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