- modeller_usage - salilab.org

AW: difference between FASTA and PDB
by Thorsten Schweikardt 07 Jul '03

07 Jul '03

Hello YeBin, Modeller states that you have more aminoacids in the alignment than in the pdb-file (353/352), and if you compare the fasta-sequence and the pdb-file you will find a lysine (K) at the C-terminus that is not present in the pdb-file. Delete the K from your alignment or change it to a "-" and Modeller should work fine. Remember that there might no be all aminoacids present in a pdb-file for structural reasons: loops at the surface may be highly mobile, and can therefore often not be solved by crystallography, and that means you will have a gap in the structure. Before modelling, check the sequence. You can use DeepView to write out the aminoacids present in the pdb-file by loading the protein and then saving the sequence in FASTA-format. Best wishes, Thorsten

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B-factor column
by Margot Ernst 07 Jul '03

07 Jul '03

Hi Modeller community, unfortunately I have not received any answer, so I will repeat my question as I REALLY would like to know: What is the value in the B-factur column of the structure files Modeller generates? Thanks for your help, margot -- ----------------------------------------------------------------- | Dr. Margot Ernst | Abteilung Prof. Sieghart | Institut f. Hirnforschung/brainresearch institute | Spitalgasse 4 | A-1090 WIEN VIENNA, Austria | margot.ernst(a)univie.ac.at | visit http://www.univie.ac.at/brainresearch ----------------------------------------------------------------- the bottom line to brainresearch: If the brain was so simple that you could understand it, you would be so simple that you couldn't. (unknown) --------------------------------------------------------- "Research: If it worked the first time, they would just call it 'search'." -Roy Garcia -------------------------------------------------------- -----------------------------------------------------------------

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FW: difference between FASTA and PDB
by Modeller Care 06 Jul '03

06 Jul '03

------ Forwarded Message From: "truename" <yb_108(a)yeah.net> Date: Sun, 6 Jul 2003 23:03:36 +0800 (CST) To: modeller-care(a)salilab.org Subject: difference between FASTA and PDB Hi!Everybody: I download the sequence of 1air in the form of FASTA and structure of it in the form of PDB for PDB.However,when I run mod.exe to build a protein modler using 1air as a template, I got error message as following ________________________ check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1AIR_.pdb rdabrk__290E> Number of residues in the alignment and pdb files are different: 353 352 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 _________________________________________ Are anybody who can solve this problem for me? Thanks alot YeBin ------ End of Forwarded Message

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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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log file
by truename 30 Jun '03

30 Jun '03

I do not know how to obtain a log file with error message with in it. Are there anybody who can help me? YeBin

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B factor column?
by Margot Ernst 30 Jun '03

30 Jun '03

Hello, apologies if this is covered in the documentation, I didn't find it: What is in the B-factor column of the PDB files Modeller writes? Thanks, margot -- ----------------------------------------------------------------- | Dr. Margot Ernst | Abteilung Prof. Sieghart | Institut f. Hirnforschung/brainresearch institute | Spitalgasse 4 | A-1090 WIEN VIENNA, Austria | margot.ernst(a)univie.ac.at | visit http://www.univie.ac.at/brainresearch ----------------------------------------------------------------- the bottom line to brainresearch: If the brain was so simple that you could understand it, you would be so simple that you couldn't. (unknown) --------------------------------------------------------- "Research: If it worked the first time, they would just call it 'search'." -Roy Garcia -------------------------------------------------------- -----------------------------------------------------------------

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FW: top file problem
by Modeller Care 28 Jun '03

28 Jun '03

Forwarded by list-owner: ------ Forwarded Message From: "truename" <yb_108(a)yeah.net> Date: Sat, 28 Jun 2003 17:48:51 +0800 (CST) To: "modeller care" <modeller-care(a)salilab.org> Subject: Re: your modeller question Dear Ursula Pieper: Thank you for your reply! How ever both the sequence that I used to align and pdb file are from the PDB.They are exactly corrospondent file for the same protein. The content of p.top are as following ___________________________________________________________________________ # 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 = './:../1DBG_A 1AIR_' # 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 ___________________________________________________________________________ and my p.aln file are as follwing ___________________________________________________________________________ >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* ___________________________________________________________________________ Best Regards YeBin Error message: > However, some difficulties confronted me during my first project of > protein modelling. Do you lend me a hand to solve it? > The error messages are as following: > ________________________________________________ > rdpir____648E>Alignment sequence not found in PDB file: 1 ./1AIR.atm > recover_____E>ERROR_STATUS >=STOP_ON_ERROR: 1 1 > > And p.top and p.ali are included in the attachment > > Thanks a lot! > Best regards > > YeBin > > > ------ End of Forwarded Message >

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