October 2003 - modeller_usage

set sequence
by Robert Farley 16 Oct '03

16 Oct '03

I am new to Modeller and am running it under Windows XP. I have little experience with computer programming, but I was able to get the model-default example using 5fd1 and 1fdx in the examples\tutorial-model directory to run OK. Now as a test of my system, I want to try to model a short 25 amino acid stretch from a test protein on the crystal structure of a related protein that is about 400 residues long. I am trying to write a top script based on the 5fd1 and 1fdx example but I do not have a pdb name for my test protein in the SET SEQUENCE line of the program since it has not been crystallized. Can someone tell me what this command does, and how I might get around this problem? Thanks for your help. RAF

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How to discard overhangs in target sequence
by Markus Fischer 16 Oct '03

16 Oct '03

Hello modellers, if my target sequence is longer compared to the template sequence and in the alignment I find an overhang for the target sequence at the N- and C-terminus, is there any way to tell modeller by some parameters to use only the part of the target sequence covered by the template, or do I have to cut the overhang in the alignment? Thanks, Markus. -- Markus Fischer Institute of Technical Biochemistry University of Stuttgart, Allmandring 31 D-70569 Stuttgart, Germany Phone: (+49)-711-685-7481 Fax: (+49)-711-685-3196 E-Mail: Markus.Fischer(a)po.uni-stuttgart.de

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HSE problem solved, new question
by Oliver Hucke 16 Oct '03

16 Oct '03

Dear modellers, two days ago I posted a message about the problem to define Histidine residues with the proton at NE2 instead of ND1. Meanwhile I found out that this can be done by patching the HIS residue with HS2 like this in the special_patches subroutine: PATCH RESIDUE_TYPE = 'HS2', RESIDUE_IDS = 'His number' Now I would like to ask some questions on the content of the *.log modeller output file: o I include some conserved water molecules in my model. This leads to the warning: iatmcls_286W> MODEL atom not classified: TIP3:OH2 TIP3 o I patch termini with the patch residues ACE and CT3, leading to similar warnings like: iatmcls_286W> MODEL atom not classified: LEU:CAY LEU iatmcls_286W> MODEL atom not classified: LEU:CY LEU iatmcls_286W> MODEL atom not classified: LEU:OY LEU For a HETATM residue that I added to the topology file no such warnings are produced. Any hints on this? Thanks a lot, Oliver -- _______________________________________ Oliver Hucke (PostDoc) Biomolecular Structure Center Dept. of Biochemistry University of Washington Health Sciences Building K-418C 1959 NE Pacific St Seattle, WA 98195 T:(206)685-7046 _______________________________________

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Problem in SEQUENCE_SEARCH
by Jorge Hernanez Fernandez 14 Oct '03

14 Oct '03

Dear Modellers!!: Is any expertise in the use of the command SEQUENCE_SEARCH ? All the time I use, the program stop trying to read the CHAINS_all.seq file. Is any kind of problem in the file? I will appreciate any help in this task. Thanks in advance: Jorge H.F. Top file is: INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ATOM_FILES_DIRECTORY = '/export/db/pdb' SET OUTPUT = 'SHORT' # 'LONG' SET SIGNIF_CUTOFF = 8 3 SET SEARCH_RANDOMIZATIONS = 10 SET STOP_ON_ERROR = 2 SET FAST_SEARCH = ON SET DATA_FILE = ON CALL ROUTINE = 'sequence_srch', SEGFILE = 'DNApol.txt', SEQUENCE = 'DNApol' The .log file all the time stop in the : BLA, BLA, BLA, Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//CHAINS_3.0_40_XN.cod Dynamically allocated memory at amaxchn [B,kB,MB]: 2306323 2252.269 2.199 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//CHAINS_3.0_40_XN.cod openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//CHAINS_all.seq -- == Dr. JORGE HERNANDEZ FERNANDEZ == ===== Lab. de Biofisica e Bioquimica ===== ===== CAT-CEPID - Instituto Butantan ===== ====== Ave Vital Brasil, 1500 S.P. ====== ==== S.B.I.- EMBRAPA - BioInformatica ==== C.p. 6041 Cidade Universitária "Zeferino Vaz" ===== Barão Geraldo Campinas S.P. ====== =========== 13080-970 ============== Tel: 0XX19-37895828 Cell: 0XX19-91336950 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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good book on modeller usage
by rathan kar 13 Oct '03

13 Oct '03

hi everyone iam a new comer for this site and for the usage of modeller. i use windows as the OS for modeller and hve downloaded it too. bt i dont find any good material over the net.plz suggest me any books for modeller programiing in windows OS if anybody knows. the current material provided by the make is not sufficient as it dosent help me in understanding the programs. also is there any hgood book on structural biology with regards Yahoo! India Matrimony: Find your partner online.Post your profile.

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HSE residue type problems
by Oliver Hucke 13 Oct '03

13 Oct '03

Dear modellers, I am trying to build an all atom protein model. Therefore I did an analysis of the Histidine types in my template structure and assigned the types HIS, HSE and HSP to the template and the conserved residues in the target sequence. When I try to model the protein with HSE residues I get the following warnings for each HSE: iatmcls_286W> MODEL atom not classified: HSE:N HSE iatmcls_286W> MODEL atom not classified: HSE:CA HSE iatmcls_286W> MODEL atom not classified: HSE:NE2 HSE iatmcls_286W> MODEL atom not classified: HSE:CD2 HSE iatmcls_286W> MODEL atom not classified: HSE:ND1 HSE iatmcls_286W> MODEL atom not classified: HSE:CG HSE iatmcls_286W> MODEL atom not classified: HSE:CE1 HSE iatmcls_286W> MODEL atom not classified: HSE:CB HSE iatmcls_286W> MODEL atom not classified: HSE:C HSE iatmcls_286W> MODEL atom not classified: HSE:O HSE Finally the calculation is terminated with the error message (see also below). getdata_289_> Proteins (all/accepted): 1 1 irestab_402W> ires, irestp: 85 26 getpdf__392E> Your library requires all bins zero; nbinx: 5 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 This is not the case if I change all the HSE's in the target sequence (one letter code '6') to HIS ('H'). Can some body give me a hint what is going on here? Your help is very much appreciated! Oliver --------------------------------------------------------------------- ----- the last section of the log file with the final error message: TOP_________> 157 118 MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_; RESTRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 30686337 29967.125 29.265 make_re_417_> Restraint type to be calculated: phi-psi_binormal openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mnch1.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mnch1.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 416 HSE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 417 PHE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 3 417 PHE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 4 417 PHE getdata_643_> Protein accepted: rat getdata_289_> Proteins (all/accepted): 1 1 irestab_402W> ires, irestp: 85 26 getpdf__392E> Your library requires all bins zero; nbinx: 5 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 -- _______________________________________ Oliver Hucke (PostDoc) Biomolecular Structure Center Dept. of Biochemistry University of Washington Health Sciences Building K-418C 1959 NE Pacific St Seattle, WA 98195 T:(206)685-7046 _______________________________________

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IC entries in topology file
by Oliver Hucke 08 Oct '03

08 Oct '03

Dear modellers, I have prepared a toplogy file for an organic molecule, but so far I omitted the internal coordinate part of the RESI entry. An optimization of the structure (short MD and final minimization) runds smoothly (no warnings or error messages) but the geometry after optimization is far from reasonable. Are the IC data needed when I start an optimization after TRANSFER_XYZ from an experimental structure? Thanks very much in advance, Oliver -- _______________________________________ Oliver Hucke (PostDoc) Biomolecular Structure Center Dept. of Biochemistry University of Washington Health Sciences Building K-418C 1959 NE Pacific St Seattle, WA 98195 T:(206)685-7046 _______________________________________

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Recent changes to the modeller_usage mailing list
by Modeller Caretaker 08 Oct '03

08 Oct '03

We have recently switched the software running at salilab.org from Majordomo to Mailman. This is to allow more fine-tuning by each user, better handling of attachments in emails and the web archives, improved support for non-English users, and easier subscribe/unsubscribes. Other than this email (and that from Mailman 'welcoming' you to the list) all else should be the same. Posts should still go to modeller_usage(a)salilab.org, and administrative queries to modeller-care(a)salilab.org. For all else, please use the web interface at http://salilab.org/mailman/listinfo/modeller_usage. A password is required to access this webpage, but this should only be 'semi-secret' - it will sometimes be emailed in the clear to you, and at any rate, if you forget it, there is a button on the web page to have it mailed to you; the password is only really to prevent other people from maliciously subscribing you to the list or altering your settings. If any problems are encountered, please let me know! Modeller Caretaker, on behalf of Andrej Sali -- 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/

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top files for ligands
by Oliver Hucke 08 Oct '03

08 Oct '03

Hi there, I am about to make a homology model of a protein with a bound substrate molecule. I would like to consider electrostatic interactions during the model refinement which means that I need a topology file for the substrate. Is somebody aware of a program that can create a charmm top file for a small organic molecule starting from the pdb file? I know that Quanta can do this but don't have access to this program. I am looking for a non-commercial program. Thanks in advance! Best, Oliver _______________________________________ Oliver Hucke (PostDoc) Biomolecular Structure Center Dept. of Biochemistry University of Washington Health Sciences Building K-418C 1959 NE Pacific Ave Seattle, WA 98195 T:(206)685-7046 _______________________________________

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Alignment
by Gianluca Ottolina 08 Oct '03

08 Oct '03

Dear Modeller user, as a newcomer I have some questions about the alignment. I use Modeller to find structure and sequence related to the target sequence as described in the chapter 1.71 of the manual (SEQUENCE_SEARCH). I obtained five new file ( .tmp; .ali; .pap; .log; and .mat) and as suggested I check for the Z-score and I find five sequence with the score more than 4. Now I would like to use these five sequence to do the alignment as suggested in the chapter 1.7.2. Is Modeller able to calculate the alignment? Yes, I think. Now the real question is how to do this alignment with ALIGN, ALIGN2D, MALIGN and MALIGN3D. I try the example reported in the manual but something is wrong and the calculation aborted all the time. Can you please post another easy example of TOP file for ALIGN and comment it; the example in chapter 2.4.14 is not clear to me. How do I use the ( .tmp; .ali; .pap; .log; and .mat) file that I obtained previously? Thanx Gianluca -- Dr. Gianluca Ottolina Istituto di Chimica del Riconoscimento Molecolare CNR Via Mario Bianco 9, 20131 Milano Italy phone 0039 02 285 000 21 fax 0039 02 285 000 36 email gianluca.ottolina(a)icrm.cnr.it web www.icrm.cnr.it

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