February 2005 - modeller_usage

Optimization or Refinement of Homology Model
by David Piper 22 Feb '05

22 Feb '05

Modellers, 1) What level of refinement or MD_LEVEL is used as a default? My top script is like this: # A sample TOP file for fully automated comparative modeling INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 2 SET ATOM_FILES_DIRECTORY = '/mod6v2/ATOMS'SET ALIGNMENT_FORMAT = 'PIR' SET ALNFILE = 'model.ali' SET KNOWNS = 'template' SET SEQUENCE = 'model' SET STARTING_MODEL=1 SET ENDING_MODEL=10 CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'special_restraints' ##there are a number of alpha helical and symmetry restraints ##omitted here for clarity. RETURN END_SUBROUTINE 2) After modelling, if there are "bumps" or poorly defined bond lengths or angles (based on ProCheck output), what is the preferred way of optimizing them? Thanks for any input, David

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(no subject)
by Mensur Dlakic 21 Feb '05

21 Feb '05

Hi all, Can someone provide an explanation about converting Modeller's dihedral restraints into plain psi/phi/omega angles? I have read through the manual and have an intuitive feel for the way Modeller calculates these values, but there are so many columns in the output file that I still am not able to decipher it. So my question is is what columns in the restraint file correspond to dihedral angles and their deviations, and how do I convert them back to numbers in the -180 to 180 range. Thanks for your help, Mensur ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic(a)montana.edu | ==========================================================================

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protein-ligand complex
by Praveen Madala 21 Feb '05

21 Feb '05

Hi Modellers, I would like to know, Is there anyway to modell a protein-ligand complex by modeller??????? If there is one, can you please tell me where can I get the information. Thanking you......... regards, Praveen On Mon, 21 Feb 2005 14:41:21 -0800 modeller_usage-request(a)salilab.org wrote: > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, >visit > http://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body >'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is >more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. setting the DEVIATION (Ori Kalid) > 2. Atom Index is out of bounds: (Amjad Farooq) > 3. Re: setting the DEVIATION (Karsten Suhre) > 4. Regarding modelling (rajesh rengaraj) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 20 Feb 2005 16:18:35 +0200 >From: "Ori Kalid" <kalido(a)mail.biu.ac.il> > Subject: [modeller_usage] setting the DEVIATION > To: <modeller_usage(a)salilab.org> > Message-ID: <00f801c51757$176c6320$551b4684@W2000EPRO> > Content-Type: text/plain; charset="windows-1255" > > Hi Everyone, > > Does anyone know how to control the XYZ randomization >parameter DEVIATION? > I tried modifying its value using a simple SET DEVIATION >= 0.0, but nothing happens. The reasults are the same as >for the default value of 4.0. > > Thanks, > > Ori > >

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Atom Index is out of bounds:
by Amjad Farooq 21 Feb '05

21 Feb '05

Dear Modeller users, I am trying to model the structure of a 300-residue protein containing a phospho-threonine (PTH). After writing the topology of PTH in top_heavy.lib and specifying PTH in restype.lib under the modlib subdirectory, I get this error upon running MODELLER: csrrng__299E> Atom index is out of bounds: 2392 2391 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 As you can see MODELLER does not complain about PTH but some general error. Has anyone encountered something like this before? How can this be fixed? Interestingly, when I substitute PTH with THR, MODELLER generates no such error and models the structure nicely. Any help will be greatly appreciated. Many thanks, Amjad **************************************** AMJAD FAROOQ PhD Assistant Professor Dept of Biochemistry & Molecular Biology Miller School of Medicine University of Miami Gautier Building, Rm 214 1011 NW 15th Street Miami, FL 33136 tel 305-243-2429 fax 305-243-3955 amjad(a)farooqlab.ws http://farooqlab.ws ****************************************

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Regarding modelling
by rajesh rengaraj 21 Feb '05

21 Feb '05

Hello modellers, Is it possible to model 1249 amino acids at a stretch by using modeller, where the target sequence is having less similarty with the template. I found the template by using the fold recognition method. Please help me modellers. --------------------------------- Do you Yahoo!? Yahoo! Search presents - Jib Jab's 'Second Term'

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setting the DEVIATION
by Ori Kalid 21 Feb '05

21 Feb '05

Hi Everyone, Does anyone know how to control the XYZ randomization parameter DEVIATION? I tried modifying its value using a simple SET DEVIATION = 0.0, but nothing happens. The reasults are the same as for the default value of 4.0. Thanks, Ori

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COVALENT_CYS
by Ori Kalid 20 Feb '05

20 Feb '05

Hi ! Does anyone know whether or not I need to use COVALENT_CYS = T when defining SS-bond PATCHes with PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = 'XXX:' 'YYY:'? Thanks, Ori Ori Kalid Dept. of Chemistry Bar-Ilan University Ramat-Gan 52900 ISRAEL Tel: 972-3-5317880 e-mail: kalido(a)mail.biu.ac.il

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Distances longer than 8.0 Angstrom?
by Amjad Farooq 18 Feb '05

18 Feb '05

Hello everyone, Does anyone know why I am getting the error message "Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:" when running MODELLER and how I can fix it. Pasted below is the MODELLER log file: --------------------------------------------------- MODELLER 7v7, Sep 12, 2004 09:15pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2004 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA 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, Linux hertz.med.miami.edu 2.6.8-1.521 i686 Date and time of compilation : 09/12/2004 21:24:59 Job starting time (YY/MM/DD HH:MM:SS): 2005/02/18 09:22:45.082 getprog_531W> ROUTINE redefined: special_restraints check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 32023 29838 csrrng__299E> Atom index is out of bounds: 2393 2391 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 15913527 15540.554 15.176 Starting time : 2005/02/18 09:22:45.082 Closing time : 2005/02/18 09:22:59.215 Total CPU time [seconds] : 11.92 ---------------------------------------------------- Many thanks, Amjad

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how to predict the model as a dimer
by Tong Chen 17 Feb '05

17 Feb '05

Hi! All: My template protein is a dimer, and the target protein is suppose to be a dimer as well. How can I get the dimer model in Modeller? Thanks a lot Tong Tong Chen School of Biological Sciences Flinders University GPO Box 2100 Adelaide 5001 Email: Tong.Chen(a)flinders.edu.au Phone: (08) 8201-3836

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redundant error check_a_337E> Structure not read in: 1
by Nicolas 16 Feb '05

16 Feb '05

Hello, I havealigned two sequences and want to modelise one of them. I applied to my file all the previous suggestions evoqued in the archive (SET OUTPUT_CONTROL = 1 1 1 1 1, corrected the format of my PIR alignement). Yet I still get the same error message. When I try to check my alignement, i also get this message. Does any body have any idea? here is the output TOP_________> 109 749 SET ALNFILE = 'ali.pir' TOP_________> 110 750 SET KNOWNS = '1ayx' TOP_________> 111 751 SET SEQUENCE = 'KPB1' TOP_________> 112 752 SET STARTING_MODEL = 1 TOP_________> 113 753 SET ENDING_MODEL = 5 TOP_________> 114 754 CALL ROUTINE = 'model' TOP_________> 115 419 CALL ROUTINE = 'getnames' TOP_________> 116 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 117 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 118 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 119 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 120 538 SET ROOT_NAME = SEQUENCE TOP_________> 121 539 RETURN TOP_________> 122 420 CALL ROUTINE = 'homcsr' TOP_________> 123 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080 openf5__224_> Open 20 OLD SEQUENTIAL ali.pir Dynamically allocated memory at amaxbnd [B,kB,MB]: 8049459 7860.800 7.677 openf5__224_> Open 20 OLD SEQUENTIAL ali.pir Read the alignment from file : ali.pir Total number of alignment positions: 500 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1ayx 446 1 glucoamlyse 2 KPB1 394 1 alpha subun TOP_________> 124 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'ne', THEN = 'GO_TO __ACCELRYS1' TOP_________> 125 117 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

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