- modeller_usage - salilab.org

residue-undefined
by Modeller Care 01 Apr '03

01 Apr '03

forwarded by the list owner ------------------------------------------------------------- Dear MODELLER users, I am facing this problem while running MODELLER. I am trying to model a protein and I want to model HEME cofactor also in the model using the template having HEME. I have indicated in the alignment file the heme symbol "h". But I am getting an error message saying residue type not defined. It dosen't say as which residue is not defined also. I could not solve the problem even after long trying. Probably it may be because of a basic mistake in the input. I would be grateful to you if any of you solve this problem. I attach the ali file top file and also the log file returned by MODELLER. Thanks. sridhar ------ End of Forwarded Message

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heteroatoms_zinc
by Alys.Peisley＠csiro.au 01 Apr '03

01 Apr '03

Hi all, i'm trying to get modeller to include a zinc atom in my model. I have mastered the art ofgetting teh zinc read into the program, however the model it produces has the zinc miles away and the coordinating residues stubbornly unligated. How does one go about instructing modeller to coordinate the zinc atom. I have a histine and a asp coordinating it. i have attached my alignment and inputfiles regards Alys [pei015@freedom model_zinc]$ more xmera_1.ali >P1;1BP3 structureX:1BP3: 214 :A: 413 :A:undefined:undefined:-1.00:-1.00 ---------------SPNKE-TF/-------------------- -------HREG--ETLM/---------------------------HFGKQYTS--MWRT/------------------------- -----------YVDVTY/-------------------------------LIDLKTGWFT/--------------- ------------FAG-Q/--------------------------KP--DHGY/----------------------/z* >P1;1N26 structureX:1N26: 92 :A: 299 :A:undefined:undefined:-1.00:-1.00 DVP--PEEPQL-SCF--------RKSPLSNVVCEWGPRSTPSLT TKAVLLV----------RKFQNSPAEDFQEPCQY--SQESQKFSC--------------QL---AVPEGDSSFYIVSMCVASSVG SKFS----KTQTFQGCGILQPDPPANITVTAVAR--NPRWLSVTWQDPH----------SWNSS-F-YRLRFELR YRAERSKTFTTW------MVKDLQHHCVIHDAWSGLRHVVQLRA--------QEEFGQGEWSEWSPEAMGTPWTES/-* >P1;1xmera sequence:1xmera: : : : :undefined:undefined:-1.00:-1.00 DVP--PEEPQL-SCFSPNKE-TF--------VCEWGPRSTPSLT TKAVLLVHREG--ETLM----------FQEPCQY--SQESQKFSCHFGKQYTS--MWRT--------------YIVSMCVASSVG SKFS----DELYVDVTYILQPDPPANITVTAVAR--NPRWLSVTWQDPHLIDLKTGWFT----------LRFELR YRAERSKTFTTWFAG-Q------QHHCVIHDAWSGLRHVVQLRAKP--DHGY--------WSEWSPEAMGTPWTES/z* the top file is [pei015@freedom model_zinc]$ more build_model.top INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'xmera_1.ali' SET KNOWNS = '1BP3' '1N26' SET SEQUENCE = '1xmera' SET HETATM_IO = on CALL ROUTINE = 'model'

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modeller question
by Modeller Care 31 Mar '03

31 Mar '03

Darren, it looks like you executed modeller without giving it a .top file. Best, ursula Forwarded by the list owner: ------ Forwarded Message From: owner-modeller_usage(a)salilab.org Date: Sun, 30 Mar 2003 18:42:39 -0800 To: modeller_usage-approval(a)salilab.org Subject: BOUNCE modeller_usage(a)salilab.org: Non-member submission from [Darren Thompson <thompson(a)chemistry.ucsc.edu>] whenever I try and run the executable mod6v2_mac10v2-absoft i get 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, Darwin Darren-Thompsons-Computer.local. 6.4 Power Mac intosh Date and time of compilation : 10/06/2002 20:50:17 Job starting time (YY/MM/DD HH:MM:SS): 2003/03/30 18:20:11.379 fullfn__230E> File not found: mod Directories: :${MODINSTALL6v2}/bin/ Extensions : .top: Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2190959 2139.608 2.089 Starting time : 2003/03/30 18:20:11.379 Closing time : 2003/03/30 18:20:14.284 Total CPU time [seconds] : 2.17 STOP and %mod6v2 usage: mod script[.top] % where is this mod script any help would be appreciated Darren A. Thompson Researcher UCSC 1156 High St. Santa Cruz, CA 95064 voice: 831-459-3390 fax: 831-459-2935 http://people.ucsc.edu/~ministry ------ 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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