- modeller_usage - salilab.org

error STDEV < 0:
by Guittet, Muriel 21 Mar '03

21 Mar '03

Dear Modellers, I saw that someone already encoutered that error in the modeller digest .. but unfortunately there was no answer (or just to use the "output='long'" command what I did without any answer) I try to model a protein structure, using 4 different templates with about 30% of sequence identity with the target. Modeller always send me the same error message: r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 stdevs__397E> STDEV < 0: -0.1509 Set to 1E-5. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Could someone explain me the meaning of this and how to fix it? thanks a lot for your help. Muriel

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Modified Protein residues
by Modeller Care 20 Mar '03

20 Mar '03

forwarded by the list owner ------------------------------------------------------------------ Dear All, My question is regarding the modelling of modified protein residues (i.e. phosphotyrosine: PTR). I know the restype.lib and Modeler libraries contain defintions for some modified residues (e.g selenomethionine) but will not contain them all. For cases like PTR, is it best to define my own residue type within the Modeler libraries or is there a simpler method? Also, I have query as to the accepted way of dealing with the format of modified residues in PDB files. In PDB files, modified residues are defined within the ATOM coordinates in the correct sequence position but labelled HETATM. I assume its ok to leave them in this format? Does Modeler read them as actual atoms or do you need to change the labelling? My apologies if the answer to this question is rather obvious, I just want to make sure I'm using the accepted format for modified residues. Many thanks, Karen -- Karen Crum Discovery Informatics Inpharmatica 60 Charlotte St London W1T 2NU www.inpharmatica.co.uk email: karen.crum(a)inpharmatica.co.uk Direct Line: 020 7074 4636 ------ End of Forwarded Message

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FW: BOUNCE modeller_usage@salilab.org: Non-member submission from ["Tsu-Sheng Wang" <tswang@life.nthu.edu.tw>]
by Modeller Care 19 Mar '03

19 Mar '03

Forwarded by the list owner. ------ Forwarded Message From: owner-modeller_usage(a)salilab.org Date: Tue, 18 Mar 2003 19:49:28 -0800 To: modeller_usage-approval(a)salilab.org Subject: BOUNCE modeller_usage(a)salilab.org: Non-member submission from ["Tsu-Sheng Wang" <tswang(a)life.nthu.edu.tw>] Dears: I think you can check MMTSB. There is a program which is caculate RMSD. The web site is http://mmtsb.scripps.edu/doc/rms.pl.html. Jack ----- Original Message ----- ±H¥óªÌ: "Shiyong Liu" <syliu(a)mdl.ipc.pku.edu.cn> œ¬¥óªÌ: "Andrej Sali" <sali(a)salilab.org>; "'quentin kaas'" <kaas(a)ligm.igh.cnrs.fr>; <modeller_usage(a)salilab.org> ¶Ç°e€é´Á: 2003œ~3€ë19€é €W€È 01:10 ¥Dœ®: source code for RMSD programme Andrej Sali,ÄúºÃ£¡ I want to caculate RMSD between one protein and many other protein structures. I hardly found a good RMSD programme by google. Could you help me give me a RMSD programme? Shiyong ======= 2003-03-18 07:02:00 ÄúÔÚÀ´‹ÅÖ‹‹´µÀ£º======= >Possibly so. > >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: owner-modeller_usage(a)salilab.org >> [mailto:owner-modeller_usage@salilab.org] On Behalf Of quentin kaas >> Sent: Tuesday, March 18, 2003 7:00 AM >> To: modeller_usage(a)salilab.org >> Subject: Re: Array too small. Increase MPAIRS >> >> >> I resolved my MPAIRS problem in using the top_heav.lib >> topology library >> instead of the top_allh.lib. As my model is quite big, the >> hydrogens may be >> too numerous to be handled by Modeller. >> Thank you for your help. >> >> Quentin Kaas >> >> Le Lundi 17 Mars 2003 16:08, Andrej Sali a écrit : >> > Without seeing the input/output files, it probably indicates a >> > difficult optimization problem that runs into many overlapping atom >> > pairs. Can you improve the alignment? >> > >> > Andrej >> >> > >. = = = = = = = = = = = = = = = = = = = = ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÖÂ Àñ£¡ ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Shiyong Liu ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡syliu(a)mdl.ipc.pku.edu.cn ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2003-03-19 ------ End of Forwarded Message

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source code for RMSD programme
by Shiyong Liu 18 Mar '03

18 Mar '03

Andrej Sali,��ã� I want to caculate RMSD between one protein and many other protein structures. I hardly found a good RMSD programme by google. Could you help me give me a RMSD programme? Shiyong ======= 2003-03-18 07:02:00 ��д��======= >Possibly so. > >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: owner-modeller_usage(a)salilab.org >> [mailto:owner-modeller_usage@salilab.org] On Behalf Of quentin kaas >> Sent: Tuesday, March 18, 2003 7:00 AM >> To: modeller_usage(a)salilab.org >> Subject: Re: Array too small. Increase MPAIRS >> >> >> I resolved my MPAIRS problem in using the top_heav.lib >> topology library >> instead of the top_allh.lib. As my model is quite big, the >> hydrogens may be >> too numerous to be handled by Modeller. >> Thank you for your help. >> >> Quentin Kaas >> >> Le Lundi 17 Mars 2003 16:08, Andrej Sali a �crit : >> > Without seeing the input/output files, it probably indicates a >> > difficult optimization problem that runs into many overlapping atom >> > pairs. Can you improve the alignment? >> > >> > Andrej >> >> > >. = = = = = = = = = = = = = = = = = = = = �� Shiyong Liu ��syliu(a)mdl.ipc.pku.edu.cn ��2003-03-19

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FW: Array too small. Increase MPAIRS
by Modeller Care 18 Mar '03

18 Mar '03

------ Forwarded Message From: quentin kaas <kaas(a)ligm.igh.cnrs.fr> Organization: CNRS - IGH Date: Fri, 14 Mar 2003 15:19:15 +0100 To: modeller-care(a)salilab.org Subject: Array too small. Increase MPAIRS I get a problem when I used Modeller when I do simple optimizations : "Array too small. Increase MPAIRS" I have seen in the archives that it was a problem with older version and I get and install the last version but it still give the same answer... Am I doing something wrong or is it a source code problem ? My top file is : SET OUTPUT_CONTROL = 1 1 1 1 1 READ_TOPOLOGY FILE = '$(LIB)/top_allh.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_MODEL FILE = '../../1hsa' READ_ALIGNMENT FILE = 'model_MHCp.ali', ALIGN_CODES = '1hsa' 'MHCp' GENERATE_TOPOLOGY SEQUENCE = 'MHCp' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE = 'MHCp.ini' MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' WRITE_RESTRAINTS FILE = 'MHCp.rsr' SWITCH_TRACE TRACE_OUTPUT = 1, FILE = 'MHCp.trc' OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20 WRITE_MODEL FILE = 'MHCp.B' Thanks in advance Quentin Kaas, IMGT ------ End of Forwarded Message

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NMR and Crystallographic models
by Simon Holton 17 Mar '03

17 Mar '03

Dear All, I am trying to construct a model of a protein based on an NMR model of a homologous protein. Having read the modeller manual I see that the structureN command can be used for NMR models, but I cannot work out how best to use it. To make the most of the NMR data regarding conformational flexibility should I split the NMR structure into separate files, each containing a single conformation, or is there a more convenient way to incorporate this information? I guess what this comes down to is how structureX and structureN are interpreted by modeller? Many thanks for your help Simon Holton ************************************************************** Dr. Simon Holton Laboratory of Molecular Biophysics, Rex Richards Building, Department of Biochemistry, University of Oxford South Parks Road Oxford Tel: 01865 275379 Fax: 01865 275182 **************************************************************

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Specification of chain of output atom files.
by Richard Friedman 14 Mar '03

14 Mar '03

Dear Modellers, How can I write a pdb file containing a chain specification? My top file is # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'monomer3.ali' # alignment filename SET KNOWNS = '1g2i' # codes of the templates SET SEQUENCE = 'prk7' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling My ali file is: C; alignment >P1;1g2i structureX:1g2i:1 :A:166 :A:Protease:Pyrococcus Horikosh: 2.00:-1.00 M---KVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDKVNPEE-FDALVLPGG RAPERVRLNEKAVS-IARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAG-VEWVDAEVVVDG NWVSSRVPADLYAWMREFVKLLK----------------* >P1;prk7 sequence:prk7:1 :A:189 :A:park7:human: 2.00:-1.00 MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGG NLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGCGSKVTTHPLAKDKMMNGGHYTYSENRVEKDG LILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD* I was hoping that inclusion of the chain designators in the prk7 sequence file, would produce a pdb file with the chain designators included, but that is not what had happened. How can I be sure that the output file includes the chain designation 'A' on every atom line? Thanks and best wishes, Rich -------------------------------------------------------------- Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Medical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman(a)cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "You don't have ot do any more work to write a book. You already wrote a book. Your course notes are a book. I've seen them lying on the floor of your office. I've seen course notes used for books on everything from Math to Origami. Just hand your course notes in. Make sure you hand in the ones with the apple juice spilled on it." -Isaac Friedman, age 13 Upon Isaac's attainment of his majority I am discontinuing the quotes from him.

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Modeller error message
by Richard Friedman 13 Mar '03

13 Mar '03

Dear Modellers, I am having difficulty getting modeller to run to completion. Here is my directory contents, my top and ali files, and an excerpt from my log file. I have also attached my complete pdb file and log file. I would greatly appreciate any suggestions as to how to get this modeller job to run to completion. My directory contents: 1g2a.atm.old 1g2i_b.pep comppdb monomer.msf park7-ig2i_b.pair park7.ssearch 1g2i.pdb 1g2i_b.tfa model-monomer.log monomer.ps park7-ig2i_c.pair xa.nrl3d.list 1g2i_a.pep 1g2i_c.pep model-monomer.top nm_007262.rsf park7.gap 1g2i_a.tfa 1g2i_c.tfa monomer.ali np_009193.rsf park7.pdb.netblastp 1g2i_b.pdb 1ga2.atm monomer.list park7-ig2i_a.pair park7.pep My top file # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'monomer.ali' # alignment filename SET KNOWNS = '1ga2' # codes of the templates SET SEQUENCE = 'prk7' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling My alignment file C; alignment >P1;1ga2 structureX:1ga2:1 : :166 : :Protease:Pyrococcus Horikosh: 2.00:-1.00 ---MKVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDK VNPE-EFDALVLPGGRAPERVRLNEKAV--SIARKMFSEGKPVASICHGPQILISAGVLR GRKGTSYPGIKDDMINAG-VEWVDAEVVVDGNWVSSRVPADLYAWMREFVKLLK------ ----------* >P1;prk7 sequence:prk7:1 : :189 : :park7:human: 2.00:-1.00 MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLED AKKEGPYDVVVLPGGNLGAQ-NLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGC GSKVTTHPLAKDKMMNGGHYTYSENRVEKDGLILTSRGPGTSFEFALAIVEALNGKEVAA QVKAPLVLKD* The error message Read the alignment from file : monomer.ali Total number of alignment positions: 190 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1ga2 166 1 1ga2 Protease 2 prk7 189 1 prk7 park7 TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1ga2.atm rdpdb___303E> No atoms were read from the specified input PDB file: 1) Possibly because an incorrect/non-existent PDB file is specified. 2) Possibly because the segment is specified incorrectly in the alignment file or by the TOP variable MODEL_SEGMENT. That is, the beginning residue number and/or chain id in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT: 1: To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 166 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 The complete log file and pdb file are attached. Thanks and best wishes, Rich -------------------------------------------------------------- Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Medical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman(a)cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "You don't have ot do any more work to write a book. You already wrote a book. Your course notes are a book. I've seen them lying on the floor of your office. I've seen course notes used for books on everything from Math to Origami. Just hand your course notes in. Make sure you hand in the ones with the apple juice spilled on it." -Isaac Friedman, age 13 Upon Isaac's attainment of his majority I am discontinuing the quotes from him.

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Modelling to multimer
by Richard Friedman 10 Mar '03

10 Mar '03

Dear Modellers, I have a monomer sequence A1 that is homologous to the monomer of a multimer structurer B1....BN. I want to build a model of the multimer B1....BN with modeller. I can think of two ways ot do this: 1. Divide the pdb files of the multimers B1....BN into single pdb files. Then I build models on A1...AN matched to them. Then I merge the A1...AN PDB files to get A1...AN. 2. Model A1 against B1. strcuturally align the structure of A1 against B1...BN. My question: is there any way that I can build the multimer A1...AN in one step against B1...BN? Thanks and best wishes, Rich -------------------------------------------------------------- Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Medical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman(a)cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "I wish that all homework was a drawing contest". -Rose Friedman, age 6

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FW: Protein+Metal Ion?
by Modeller Care 10 Mar '03

10 Mar '03

------ Forwarded Message From: Oliver Hucke <Oliver.Hucke(a)physchem.uni-freiburg.de> Date: Fri, 07 Mar 2003 10:00:39 +0100 To: Modeller Care <modeller-care(a)salilab.org> Subject: Re: Protein+Metal Ion? Dear Marc, you might define the subroutine 'special_restraints' at the end of your top script introducing the bonds between the metal ligand atoms and the metal atom in form of e.g. harmonic potentials. In my case the following introduced 6 ligand-Fe bonds: SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS 'NE2:501' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'NE2:541' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'NE2:815' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'NE2:862' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'OE1:830' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'OE2:830' 'FE2:1185' RETURN END_SUBROUTINE Note: the numbers of the residues correspond to the modeller numbering scheme. You may get the correct numbers from an *.ini file. Info on the meaning of the ADD_RESTRAINT lines can be found in the chapter "specification of restraints" in the modeller manual Hope this helps! Best, Oliver > I would like to model a protein that contains Zn in the active site. In = > the template structure, two His residues are coordinated to the Zn. The = > target sequence also has these residues and the sequences display > 50% = > identity. How do I force the His residues to similarly coordinate the = > Zn in the modelled structure? If the Zn atom is in .pdb file, modeller = > doesn't seem to notice. Without the Zn atom present, the His = > sidechains simply flop around in the active site (not surprisingly). > > Marc Campitelli -- ____________________________________________________________________________ Oliver Hucke Inst. fuer Physikalische Chemie II Universitaet Freiburg Albertstr. 23a D-79104 Freiburg Tel. : +49-761-203-5130 (/-6179) Fax. : +49-761-203-6189 email: Oliver.Hucke(a)physchem.uni-freiburg.de ____________________________________________________________________________ ------ End of Forwarded Message

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