May 2001 - 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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COMPARE scripts
by Troy Wymore 30 May '01

30 May '01

Hello Modellers, I have built a protein structure using MODELLER and would like to compare it with the actual crystal structure using the COMPARE routines. The MODELLER protein and XRAY protein have the same sequence but the MODELLER protein is numbered from 1-494 and the XRAY protein is numbered from 7-500 and contains multiple chains. So MODELLER complains: sequence difference between alignment and pdb compare_W> some residues are without DISTANCE_ATOMS[1] atom So is there something simple I can do to make this compare script work? I am thinking that I can delete the other chains and renumber the residues in the xray structure file to make it look similar to the MODELLER produced file but was hoping there was something easier to do. Any help would be much appreciated. Troy Wymore

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Orbital casino
by Orbital casino 25 May '01

25 May '01

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HETATM
by Bessie 23 May '01

23 May '01

Dear users, I am having problem with adding heteroatoms to my model. My template is a dimer with each having one inhibitor and one cofactor. I use '.' for HETATM and 'w' for water molecule in my alignment file. But each time I run, the .log file told me there are " too many non-bonded pairs. Increase MPAIRS". What does it mean? What should I do? By the way, what should the comment line be with 2 chains and 4 HETATM and one H2O all together? The last several letters of the alignment file is: DHYRY/....w* Is it right? Best Bessie

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oligomers
by Dr Nicolas Le Novere 21 May '01

21 May '01

Dear modellers, My template is a homooligomer. I would like to model similar oligomers either with N times the same sequence, or with different homologous sequences. What is the best format for the alignment and/or top (How to force MODELLER to model the sequence X on the chain A and the sequence Y on the chaine B?) Regards, -- Dr Nicolas Le Novère http://www-alt.pasteur.fr/~lenov Dpt of Zoology, Univ of Cambridge, Downing street, Cambridge CB2 3EJ, UK tel: +44 1223 336623 fax: +44 1223 336676 e-mail: nl223(a)cus.cam.ac.uk

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can't get disulfides bonds
by Dr Nicolas Le Novere 21 May '01

21 May '01

Dear modellers, [modeller6a] My template contains two disulfides bonds, and the cysteines are conserved in the protein I want to model. Hence, PATCH_SS_TEMPLATE, automatically run by the routine 'model' is suppose to take care of the bonds. It doesn't. Hence my first question: How MODELLER detect SS bonds in templates: SSBOND in the HEADER or CONECT at the end of the PDB file? Then I decided to patch the disulfides manually with INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'a7ggmono2.ali' # alignment filename SET KNOWNS = 'mono2' # codes of the templates SET SEQUENCE = 'a7gg' # 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) CALL ROUTINE = 'model' # do homology modelling STOP SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '127' '141' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '189' '190' RETURN END_SUBROUTINE It did not work either. Any ideas? -- Dr Nicolas Le Novère http://www-alt.pasteur.fr/~lenov Dpt of Zoology, Univ of Cambridge, Downing street, Cambridge CB2 3EJ, UK tel: +44 1223 336623 fax: +44 1223 336676 e-mail: nl223(a)cus.cam.ac.uk

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3d staff
by Joshua Bleeth 06 May '01

06 May '01

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