April 2000 - modeller_usage

Error using MALIGN3D
by Michael Buck 24 Jan '02

24 Jan '02

MALIGN3D Top files which worked well using Modeler 4 are giving me this error : fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am using the following script # MALIGN3D READ_ALIGNMENT FILE = 'pair.aa' SET ATOM_FILES = '1.pdb' '2.pdb' SET FIT_ATOMS = 'CA' MALIGN3D GAP_PENALTIES_3D= 0 2.0, WRITE_FIT = on, WRITE_WHOLE_PDB = off If anybody has seen this problem, please help. Thank you Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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problem!
by Paola D'Alessio 15 Jun '01

15 Jun '01

Dear users, I am trying to produce a chimeric model for my protein. The first thing I want to do is to check the alignment I have. When I tell Modeller to execute the "check_alignment" command, I get the following message: rdpir___E> alignment sequence not found in PDB file: 1 ./pXXXX.pdb ####################################################################################################################################### The alignment I have is: >P1;pXXXX structureX:pXXXX:.::.::::: CKPMSNFRF-GENHAIMGVAFTWVMALACAAPPLVGWS--RYIPEGMQC-SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTH--------QGSDFGPIFMTIPAFFAKTSAVYNPVIYIMM* >P1;pAveM structure:pAveM:2::211::::: -----------VRWAKLYSLVIWGCTLLLSSPMLV-----------------------------EVFTNMLLNVVGFLLPLSVITFCTMQ---------------------ERRATVLVLVVLLLFIICWLPFQISTFLDTL----------------VITQIASFMAYSNSCLNPLVYVIV* >P1;Ali2 sequence:Ali2:::::::: VKTMSMGRMRGVRWAKLYSLVIWGCTLLLSSPMLVFRTMKEYSDEGHNVTACVISYPSL---IWEVFTNMLLNVVGFLLPLSVITFCTMQIMQVLRNNEMQKFKEIQT---ERRATVLVLVVLLLFIICWLPFQISTFLDTLHRLGILSSCQDERIIDVITQIASFMAYSNSCLNPLVYVIV* ####################################################################################################################################### Perhaps, something is wrong with file names or PDB codes.(I stored the pdb files as pXXXX.pdb) Can somebody help me? Thank you very much, Paola -- dott. Paola D'Alessio (PhD student) Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio(a)unisa.it

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Re: multiple and not overlapping templates
by Xiao-Ping Zhang 10 Apr '00

10 Apr '00

Dear Dr. Andras Fiser, Sorry for replying you late. Thank you for your top and alignment files. They are very helpful. To compare your top file with mine, I found that I used a comma between two knows files: SET KNOWNS='template1, template2' although I don't know if it really matter. Another problem was found by using the debug option: SET OUTPUT_CONTROL= 1 1 1 1. Modeller complained that one of my template was unacceptable, probably that was because its low resolution (2.6 or something) and too many missing atoms. After changing to another template, I got model. Thank you for your help. Sincerely, Xiao-Ping At 07:05 PM 3/28/00 -0500, you wrote: > > Dear Xiao-Ping , > > It is not very fruitful, if you are not showing what exactly you are dealing > with. > > As a last help I send one of mine last application for the very same topic, > hope it helps. > a top file and an alignment file. Structures were generataed without any > problem. > > best wishes, > > Andras > > ########################################### > > INCLUDE > SET OUTPUT_CONTROL= 1 1 1 1 > SET ALNFILE='tetu.pir' > SET KNOWNS='2abc3' '2abc2' > SET SEQUENCE= 'tetu' > SET STARTING_MODEL= 1 > SET ENDING_MODEL = 30 > > CALL ROUTINE = 'model' > > > SUBROUTINE ROUTINE = 'transfer_xyz' > > # SET ALIGNMENT_FORMAT = 'PIR' > ## READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS > ## MALIGN3D FIT = off, GAP_PENALTIES_3D = 0 4 > READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE > > READ_TOPOLOGY FILE = TOPLIB > READ_PARAMETERS FILE = PARLIB > > CALL ROUTINE = 'create_topology' > > TRANSFER_XYZ CLUSTER_CUT = -1.0 > BUILD_MODEL INITIALIZE_XYZ = OFF > > WRITE_MODEL FILE = MODEL > > RETURN > END_SUBROUTINE > ################################################## > > >P1;2abc3 > structureX:2ezm3:55::99::::: > ----YPSDNEEFDPHEQEDKLADPHEQCEFDCDPYPSDNEEDYPSHEQC----------- > -----------------------------------------* > >P1;2abc2 > structureX:2ezm2:5::48::::: > -------------------------------------------------------SQTCY > LSDKEYHRTCNMKHGSDFEQAPLPWDFHGKLMNYTELKS--* > >P1;tetu > sequence:tetu:::::::: > DCDPKLADNEEDEFDCDPNEEFDPHEDKLADPHEQCEFDCDPYPSDNEEDYPSDNEEDKL > NSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKYE* > > ################################################# > > > -- > , > Andras Fiser, PhD # phone: (212) 327 7206 > The Rockefeller University # fax: (212) 327 7540 > Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu > New York, NY 10021-6399, USA # http://salilab.org/~andras ------------------------------------------------ Xiao-Ping Zhang Department of Biochemistry Stockholm University 106 91 Stockholm Sweden Phone: 46-08-162582 / 162472 Fax: 46-08-153679 e-mail: zhang(a)biokemi.su.se

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[Fwd: Core dump with Modeller on Linux]
by Andras Fiser 07 Apr '00

07 Apr '00

1 0

Core dump with Modeller on Linux
by David Chalmers 06 Apr '00

06 Apr '00

Hi all, I am trying to run Modeller on a linux box but all of the executables I have downloaded core dump. Do I need a new password? I am running plain Redhat 6.1. I have installed the f2c libraries using f2c-19990728-1.i386.rpm. On another note. How do you get to the year 2000 archives of the modeller list? There are only links to 1999 and 1998 as far as I can see. Best wishes and thanks for the use of a very useful program! David _____________________________________________________________________________ David Chalmers Lab: 9903 9110 Victorian College of Pharmacy Fax: 9903 9582 381 Royal Pde, Parkville, Vic 3053 http://synapse.vcp.monash.edu.au Australia David.Chalmers(a)vcp.monash.edu.au _____________________________________________________________________________

1 0

None
by Bogdan Morgun 05 Apr '00

05 Apr '00

1 0

Sequence file problem
by Troy Wymore 04 Apr '00

04 Apr '00

Hello MODELLERs, I am new to MODELLER and would like to know if there is an easy way to accomplish this task. I have a raw sequence that I want to align with my 3D structural alignment that contains nine sequences. First, it seems like my raw sequence should be formatted so that MODELLER can read it. Since this is just a sequence with no corresponding structure shouldn't the second line of the sequence file just be: sequence: It seems strange to me that in the manual all the examples of sequences have a corresponding PDB code when the point of homology modelling is to create the model hence no PDB code. Or for this do I just make one up? If the sequence file for the target is then correct can I do the following: READ_ALIGNMENT FILE = 'structures3d.ali', ALIGN_CODES = 'all' # my 3D # structural alignment for nine structures SET ADD_SEQUENCE = on, ALIGN_BLOCK = NUMB_OF_SEQUENCES READ_ALIGNMENT FILE = 'sequence.ali', ALIGN_CODES = 'all' # my target # sequence SET OVERHANG = 0 ALIGN2D GAP_PENALTIES_1D= -400 -150, GAP_PENALTIES_2D = 0.5 0.5 0.5 0.5 0.5 6 Any advice would be much appreciated. General strategies that accomplish the same basic task but don't address my specific problem are also welcome. Troy Wymore Biomedical Initiatives Group Pittsburgh Supercomputing Center

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