modeller_usage July 2003

modeller_usage@salilab.org

19 participants
24 discussions

Error on reading ligands
by Modeller Care 06 Jul '03

06 Jul '03

Non member submission forwarded by listowner ------ Forwarded Message From: owner-modeller_usage(a)salilab.org Date: Wed, 2 Jul 2003 09:00:22 -0700 To: modeller_usage-approval(a)salilab.org Subject: BOUNCE modeller_usage(a)salilab.org: Non-member submission from [Aldo Jongejan <jongejan(a)few.vu.nl>] From: Aldo Jongejan <jongejan(a)few.vu.nl> Dear readers, I have specified a ligand for use in the modelling procedure along the lines of the answer to FAQ 17. However, I get an error: 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 ---------------------------------------------- 446 1 327 334 K I 14.724 END OF TABLE patch_s_522_> Number of disulfides patched in MODEL: 1 delete__442E> One or more atoms absent from MODEL: O: 445: C: 445: N: 446: CA: 446: I have specified the PATC FIRS NONE LAST NONE in the top_heav.lib, so I expected this residue to be on its own and have no links to the protein. It seems that MODELLER wants to link the residue to the Cterm. How can I prevent this? The last part of my alignment is as follows: EHCWK------------------------------------/i* But substituting / by - does not help either. In the PDB file for the structure the ligand is now specified forming a separate chain. Can somebody help me with this problem?? with kind regards, aldo -- /////////////////////////////////////////// NOTE: E-mail address has changed into jongejan(a)few.vu.nl /////////////////////////////////////////// ########################################### Aldo Jongejan Molecular Modeling Group Dept. of Pharmacochemistry Free University of Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands e-mail: jongejan(a)few.vu.nl tlf: +31 (0)20 4447612 fax: +31 (0)20 4447610 ########################################### ------ End of Forwarded Message

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Re: make a model from two X-ray structures which has no overlap
by Modeller Care 03 Jul '03

03 Jul '03

non member submission forwarded by list owner: ------------------------------------------------------------ On 7/3/03 12:35, "Hai-Long Wang" <hwang(a)mayo.edu> wrote: > Dear Modeller > > I am try to built a homology model from two different x-ray structures. > these x-ray structures represent two parts of my model, and they have no > common part. but need to be fit togather. I had hard time to built a > reasonable model with two parts fit. seems the interface really block the > two parts to be togather. Any one who has done this before? Please give me > some clue! > > Thanks > > HL Wang >

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My 1DBG_A.pdb
by truename 03 Jul '03

03 Jul '03

Hi! My 1DBG_A.pdb was included in attachment YeBin

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Incorrect PDB file
by truename 01 Jul '03

01 Jul '03

Hi!Everybody: Is there anybody who can correct this error for me? My error messages are as following __________________________________ openf5__224_> Open 11 OLD SEQUENTIAL ./1DBG_A.pdb rdpdb___303E> No atoms were read from the specified input PDB file: 1) Possibly because an incorrect/non-existent PDB file is specified. 2) Possibly because the segment is specified incorrectly in the alignment file or by the TOP variable MODEL_SEGMENT. That is, the beginning residue number and/or chain id in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT: 1: To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 506 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 ___________________________________________________________ and my top file ___________________________________________________________ # Very fast homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET ALNFILE = 'Together2.ali' # alignment filename SET KNOWNS = '1DBG_A' '1AIR_' # codes of the templates SET SEQUENCE = 'T0101' # code of the target SET ATOM_FILES_DIRECTORY ='./:../atom_files' # directories for input atom files SET STARTING_MODEL = 2 SET ENDING_MODEL = 2 SET OUTPUT_CONTROL = 1 1 1 1 2 # SET OUTPUT = 'LONG' SET FINAL_MALIGN3D = 1 CALL ROUTINE = 'very_fast' # prepare for extremely fast optimization CALL ROUTINE = 'model' # do homology modelling ________________________________________________________________ My alignment file ______________________________-- >P1;1DBG_A structureX:1DBG_A:1 : :506 : : : : : ----MKMLNKLAGYLLPIMVLLNVAPCLGQVVASNETLYQVVKEVKPGGLVQIADGTY-- -----KDVQLIVSNSGKSGLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWFKDGNRA IQAWKSHGPGLVAIYGSYNRITACVFDCFDEANSAYITTSLTEDGKVPQHCRIDHCSFTD KITFDQVINLNNTARAIKDGSVGGPGMYHRVDHCFFSNPQKPGNAGGGIRIGYYRNDIGR CLVDSNLFMRQDSEAEIITSKSQENVYYGNTYLNCQGTMNFRHGDHQVAINNFYIGNDQR FGYGGMFVWGSRHVIACNYFELSETIKSRGNAALYLNPGAMASEHALAFDMLIANNAFIN VNGYAIHFNPLDERRKEYCAANRLKFETPHQLMLKGNLFFKDKPYVYPFFKDDYFIAGKN SWTGNVALGVEKGIPVNISANRSAYKPVKIKDIQPIEGIALDLNALISKGITGKPLSWDE VRPYWLKEMPGTYALTARLSADRAAKFKAVIKRNKEH* >P1;T0101 sequence:T0101:1 : :400 : : : : : ADCSSDLTSGISTKRIYYVAPNGNSSNNGSSFNAPMSFSAAMAAVNPGELILLKPGTYTI PYTQGKGNTITFNKSGKDGAPIYVAAANCGRAVFD----------FSFPDSQWVQAS--- --------------YGFYVTGDYWYFKGVEVTRAGYQGAYVIGSHNTFENTAFHHN---- ----------RNTGLEINNG--GSYNTVINSDAYRNYDPKKNGSMADGFGP-KQKQGPGN RFVGCRAWENSDDGFDLFDS--PQKVVIENSWAFRNGINYWNDSAFAGNGNGFKLGGNQA VGN-------HRITRSVAFGNVSKGFDQNNNAGGVT---------------VINNTSYKN GINYGFGSNVQSGQK----------------------HYFRNNVSLSASVTVSNADAKSN SWDTGPAASASDFVSLDTSL------------------------ATVSRDNDGTLPETSL FRLSANSKLINAGTKESNISYSGSAPDLGAFERN---* >P1;1AIR_ structureX:1AIR_:1 : :353 : : : : : ---------ATDTGGYAATAGGNVTGAVSKTATSMQDIVNIIDAARLDANGKKVKG---- -----GAYPLVITYTGNEDSLINAAAAN--------------------ICGQWSKDPRG- --------------VEIKEFTKGITIIGANGSSANFGIWIKKSSDVVVQNMRIGYLPGG- ----------AKDGDMIRVD--DSPNVWVDHNELFAANHECDGTPDN-----------DT TFESAVDIKGASNTVTVSYN-----YIHGVKKVGLDGSSSSDTGRNITYHHNYYNDVNAR LPLQ-------RGGLVHAYNNLYTNITGSGLNVRQN------------------GQALIE NNWFEKAINPVTSRY--------------------------DGKNFGTWVLKGNNITKPA DFSTYSITWTADTKPYVNAD---------------------------SWTSTGTFPTVAY N----YSPVSAQCVKDKLPGYAGVGKNLATLTSTACK* ______________________________________________________ My PDB files and sequences used in the alignment are all from PDB Any help would be appreciated. YeBin

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modeller_usage July 2003