March 2003 - modeller_usage

FW: Modeller6v2 trouble
by Modeller Care 12 Jun '03

12 Jun '03

------ Forwarded Message From: Mario Garcia <sbioi000(a)cib.csic.es> Date: Fri, 21 Mar 2003 16:53:17 +0100 (CET) To: modeller-care(a)salilab.org Subject: Modeller6v2 trouble Dear Dr. Bozidar, I have some error after a modeling jot execution (mod script.top) in Modeller6v2 under an IRIX 6.2 box. Bellow, I include the corresponding .top and .ali input files and the resulting .log file. Could you give some hints to help me? Thank you very much in advance for your help. Regards, Mario Garcia. ------------------------------------------------------------------------- Mario Garcia de Lacoba, PhD. Phone : +341 915611800 (ext.4334) Fax : +341 915627518 Centro de Investigaciones Biologicas E-mail : mario(a)cib.csic.es C.S.I.C. c/ Velazquez, 144 28006-Madrid. SPAIN. ------------------------------------------------------------------------- ======================MOB3.top=================================== # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'MOB4.ali' # alignment filename SET KNOWNS = '1cii' # codes of the templates SET SEQUENCE = '1mob' # 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) CHECK_ALIGNMENT CALL ROUTINE = 'model' # do homology modelling ================MOB4.ali================================ C; mob_1cii.phy align >P1;1cii structureX:1cii EIMAVDIYVNPPRVDVFHGTPPAWSSFGNKTIWGGNEWVDDSPTRSDIEK RDKEITAYKNTLSAQQKENENKRTEAGKRLSAAIAAREKDENTLKTLRAG NADAADITRQEFRLLQAELREYGFRTEIAGYDALRLHTESRMLFADADSL RISPREARSLIEQAEKRQKDAQNADKKAADMLAEYERRKGILDTRLSELE KNGGAALAVLDAQQARLLGQQTRNDRAISEARNKLSSVTESLNTARNALT RAEQQLTQQKNTPDGKTIVSPEKFPGRSSTNDSIVVSGDPRFAGTIKITT SAVIDNRANLNYLLSHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEVAE WDKLRQRLLDARNKITSAESAVNSARNNLSARTNEQKHANDALNALLKEK ENIRNQLSGINQKIAEEKRKQDELKATKDAINFTTEFLKSVSEKYGAKAE QLAREMAGQAKGKKIRNVE-EALKTYEKYRADINKKINAKDRAAIAAALE SVKLSDISSNLNRFSRGLGYAGKFTSLADWITEFGKAVRTENWRPLFVKT ETIIAGNAATALVALVFSILTGSALGIIGYGLLMAVTGALIDESLVEKAN KFW* >P1;1mob sequence:1mob ------MSYMVARMQKMKAGNLGGAFKHNERVFETHSNKDINPSRSHLN- --YELTDRDRSVSYEKQIKDYVNENKVSNRAIRKDAVLCDEWIITSDKD- -----------FFEKLDEEQTRTFFETAKNYFAENYG-ESNIAYASVHLD ESTPHMHMGVVPFENGKLSSKAMFDREELKHIQEDLPR--YMSDHGFELE -------------------------------RGKLNSEAKHKTVAEFKRA MADMELKEELLEKYHAPLFVDERTG--ELNNDTEAFWHEKEFADMFEVQS PIRETTNQEKMDWLRKQYQEELKKLESSKKP-LEDDLSHLEELLDKKTKE YIKIDSEASERASELSKAEGYINTLEN--HSKSLEAKIECLESDNLQLEK Q----KATKLEAKALNES----ELRELKPKKNFLGKEHYELSPEQ---FE GLKAEVYRSRTLLHHKDIELEQAKRQVSLRASKNYFTASLERAKEKAKGE SIDR--LKSEIKRLKN------------E----N-SILRQQNDK-MLGKL RELMPDKAFKNLLSELKAIKP-----------IVNIIKKAIEKSLF---- ---* =====================MOB4.log================================= MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, IRIX64 akilonia 6.5 IP30 Date and time of compilation : 07/05/2002 17:12:26 Job starting time (YY/MM/DD HH:MM:SS): 2003/03/21 23:47:53.033 TOP_________> 105 705 SET ALNFILE = 'MOB4.ali' TOP_________> 106 706 SET KNOWNS = '1cii' TOP_________> 107 707 SET SEQUENCE = '1mob' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND check_a_335E> No alignment. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2003/03/21 23:47:53.033 Closing time : 2003/03/21 23:48:02.202 Total CPU time [seconds] : 0.00 ------ End of Forwarded Message

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modeller from python
by Ursula Pieper 31 Mar '03

31 Mar '03

Abhinav, We don't have experience with python, but my guess is that some environment variables are not set properly. Best regards, Ursula --- Ursula Pieper temporary modeller caretaker Message forwarded by the listowner: ------------------------------------------------------------------------ Dear Andrej, I am having a small problem regarding running modeller from a python script. Can you let me know some solution. The program terminates after generating .ini file. Do I need to run modeller from command line only. I use the system commands in python script(os.system('mod6v2 xyz')) Hoping to hear from you soon. Best Regards, Abhinav.

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MAXATM
by Matteo Masetti 31 Mar '03

31 Mar '03

Dear all, I am using Modeller6v2 running on a PC Linux machine (OS RedHat 8.0; kernel version 2.4.28), and i'm trying to build the model of a symmetric tetrameric protein. I met the following problem: after the building of 2 models out of ten, modeller stops with the following error message: define__223E> Array too small. Increase MAXATM current maximum, current need: 3228 3229 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 We don't have the source files: please, may you help me?

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Re: Re: Modeller6v2 installation problem
by Kong Lesheng 23 Mar '03

23 Mar '03

Dear Dr. Bozidar Yerkovich, I have added RTF of HYP into Modeller6v2 library. With best regards, Kong Lesheng --------------------------------- BioInformatics Center National University of Singapore 10 Kent Ridge Cresent Singapore119260 Tel: (65)6874 4459 Fax: (65)6778 2466 ---------------------------------

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Re: Re: Modeller6v2 installation problem
by Kong Lesheng 23 Mar '03

23 Mar '03

Dear Dr. Bozidar Yerkovich, I have added RTF of HYP into Modeller6v2 library. With best regards, Kong Lesheng --------------------------------- BioInformatics Center National University of Singapore 10 Kent Ridge Cresent Singapore119260 Tel: (65)6874 4459 Fax: (65)6778 2466 ---------------------------------

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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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