January 1999 - modeller_usage

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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Refinement from my own initial Structure
by Tony Pemberton 29 Jan '99

29 Jan '99

Dear Modeller users, I have been having problems carrying out a refinement from my own initial structure. I have adopted the steering file example from FAQ no. 12, but my procedure is resulting in the .ini file being overwritten. I want to produce a model based on some templates, but want to carry out the procedure in two stages. The first stage should be to achieve the overall fold based on the templates. The second stage is to refine part of the target based on another alignment which should produce (I hope) better results in that part of the target. To put it another way, this is a bit like the chimera example in FAQ no. 4, except that I think I can get the overall fold by the two stage process outlined above (the problem in FAQ no. 4). Here is my steering file for the second stage: # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET ALNFILE = 'seq.pir' # alignment filename SET KNOWNS = '1abc' '1cde' '1fgh' # templates SET SEQUENCE = '1ijk' # target SET ATOM_FILES_DIRECTORY = './' # directories SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 3 # index of the last model SET DEVIATION = 4.0 # has to be >0 if more than 1 model SET RAND_SEED = -12312 # to have different models from # another top SET MD_LEVEL = 'refine3' # what kind of optimization is done # Specifiying an alternate starting structure. # Specify the initial structure filename, and tell the program to # read the initial file, not construct it from the templates: # ref.ini is my model from stage one # SET MODEL = 'ref.ini', BUILD_METHOD = 'read_xyz' # Homology modelling by the MODELLER TOP routine 'model'. # Demonstrates how to refine only a part of the model. SET DYNAMIC_FLAG = 0 # selected atoms do not feel the #neighbourhood CALL ROUTINE = 'model' # do modelling on supplied modelling # (hopefully) # select the residues for second stage refinement SUBROUTINE ROUTINE = 'select_atoms' PICK_ATOMS SELECTION_SEGMENT='17:' '43:', SELECTION_SEARCH='segment', ; PICK_ATOMS_SET=1, RES_TYPES='all', ATOM_TYPES='all', ; SELECTION_FROM='all', SELECTION_STATUS='initialize', SELECTION_STEP=1 RETURN END_SUBROUTINE ####################################################### I assumed that "BUILD_METHOD = 'read_xyz'" was a flag to modeller that tells it *not* to construct an initial model from the templates, but to read the .ini file supplied. Correct? (y/n) The result of the above is to construct both a new .ini file with part of the molecule built from topology (extended chain) and the same for the resultant structure, but with the rest refined as I wanted. That is, I get the refinement I wanted but lose the overall fold from stage one. Can anyone tell me where I am going wrong, Regards, Tony Pemberton ********************************************************************* Mr. A.J.Pemberton Tel: +44 121-414-3388 c/o Dept. Rheumatology, Fax: +44 121-414-3982 Medical School, E-mail: A.J.Pemberton(a)bham.ac.uk The University of Birmingham, Birmingham B15 2TT. U.K. *********************************************************************

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MODELLER and external constraints (such as NMR)
by chunhua yuan 26 Jan '99

26 Jan '99

Dear MODELLER users: I wonder whether anyone have tried to incoporate external constraints such as those from NMR in modeling. I have some NMR constraints derived from NOE and want to incorporate them into molecular dynamics step, but have no idea how to get start, such as the format (page 72 manual) and the command in TOP file. By the way, I have got the model using "fully automated comparative modeling." Thanks for any comments. Best regards, Chunhua Yuan

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Re: Modeller: too many parameters?
by Andrej Sali 08 Jan '99

08 Jan '99

Also, if you are using more than 1 templae, it could be that they are aligned such that equivalent distances in the templates are more than say 5 angstroms different. Check the output of CHECK_ALIGNMENT in the log file please. If this is so, that would also increase the number of parameters needed for the splined restraints (fixed dx). Andrej szia(a)hanga.enzim.hu wrote: > > Hi, > > > Please try > > > > SET SPLINE_ON_SITE = off > > > > before CALL ROUTINE = 'model'. > > Thanks. The program seems to be running now, apart from the fact that it > writes some hundreds of thousands of warnings of the following type to the > log file: > > chkder___W> DVY(i) out of bounds: 6646 6646 0.1013E+13 > > But Andras Fiser was here the day before yesterday and he told me that > this is not an actual problem. > > > Can I put this onto the MODELLER usage mailing list? > > Yes, of course. > > Best, > Andras > > Andras Szilagyi (szia(a)enzim.hu) > Institute of Enzymology, Hungarian Academy of Sciences > Karolina ut 29., H-1113 Budapest, HUNGARY > Fax: +36 1 166 5465, phone: +36 1 166 5633 -- Andrej Sali, Assistant Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockvax.rockefeller.edu; http://salilab.org

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[Fwd: Modeller: too many parameters?]
by Andrej Sali 08 Jan '99

08 Jan '99

-- Andrej Sali, Assistant Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockvax.rockefeller.edu; http://salilab.org

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[Fwd: Modeller: too many parameters?]
by Andrej Sali 08 Jan '99

08 Jan '99

-- Andrej Sali, Assistant Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockvax.rockefeller.edu; http://salilab.org

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