modeller_usage

modeller_usage@salilab.org

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3147 discussions

Enormous modeller for Linux
by Graham Tyrrell 02 Feb '99

02 Feb '99

I am currently using the ENORMOUS (2000 residue) version of Modeller4 running on an SGI. However, we have recently built a large Linux cluster, and I would like to try running Modeller on it. It appears that the compiled versions for Linux at the ftp site only allow up to 1000 residues which is of little/no use to me as I am modelling a 1200 residue protein. Any possibility of an ENORMOUS version for Linux? (presumably, available memory is a large constraint... what kind of requirements does Modeller have?) Regards Graham Tyrrell -- ---------------------------------------------------------------------- Graham Tyrrell Email (Work) : tyrrell(a)yorvic.york.ac.uk (Personal) : gpt103(a)york.ac.uk Telephone : (01904) 432550 -----------------------------------------------------------------------

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Defining Custom residues
by David Chalmers 01 Feb '99

01 Feb '99

Hi All, I am having some difficulties defining my own residues for use with Modeller4. Despite reading the FAQ and the other documentation Modeller does not seem to recognise my residues. Does anybody have an example of a protein containing a custom residue or ligand that I could study to see if I am doing the right things? Thanks for any help that anyone can provide, 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 _____________________________________________________________________________

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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

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Problems using more than two templates
by Thorsten Schweikardt 18 Dec '98

18 Dec '98

Dear Modellers, I am having a similar problem as Susan Crennell, whose mail you answered on Nov, 3 . Unfortunately, your advice to correct the alignment does not work in my case. I am trying to model certain loops into an incomplete PDB-file using other PDBs of related proteins as templates for the loops. I used the following top-file: INCLUDE SET ALNFILE = 'WXY.ali' SET KNOWNS = 'w' 'x' 'y' SET SEQUENCE = 'target' SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL= 1 SET ENDING_MODEL = 3 SET OUTPUT_CONTROL = 1 0 1 1 SET MD_LEVEL = 'refine1' SET RSTRS_REFINED = 2 CALL ROUTINE = 'model' with 3 templates (W, X, Y) and 1 target-sequence (each chain contains ~650 AA), with Y as the incomplete PDB-file, X a different PDB of the same (!) protein and W a related protein. WXY.ali: P1;w (structure related to Y and X) structure:w:1::660::::: WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW-WWWWWWWW---WWWWWWW--WWWWWWWWWW* P1;x (same structure as Y, but different pdb-file) structure:x:1::660::::: ------XXXXXXXXX---XXXXXXXXX-XXXX----XXXXXXXXXXX--XXXXXXXXX--XXXXXXXXXXXXXX* P1;y (known structure) structure:y:1::650::::: ------YYYYYYYYY-----YYYYYYYYYY-----YYYYYYYYYYYY--YYYYYYYYY--YYYYYYYYYYYYYY* P1;target (sequence of known structure Y, including missing AA) sequence:target:::::::: ------TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT--TTTTTTTTT--TTTTTTTTTTTTTT* I called up modeller (Version: mod_iris4d-IRIX5.3) under IRIX6.2 . Approximately 15 min. after the initial model is written, Modeller4 cancels with an error in the log-file: ... getrsr___> Numb of previous, current selected restraints: 56430 68752 mkspline_E> too many parameters, increase MPRMCNS This error does _not_ occur when there are 5 templates, and 4 of them are identical: SET KNOWNS = 'w' 'y' 'y' 'y' 'y' or 4 templates, and 3 of them are identical (etc...) SET KNOWNS = 'w' 'y' 'y' 'y' In these cases, I am getting an output with no errors at all, and with a good-looking result, but as soon as I am trying to implement a third template, the described error occurs. What confuses me is the fact, that when I use just _two_ of these together, there are no problems, no matter which templates I choose: W and X : works (ini-file, restraints-file and schedule-file were written out) Y and X : works (same as above) W and Y : works (same as above); Using all three of them together seems to be impossible. I thought, if there was a problem, then it was because of the slight structure change between Y and X: maybe the difference was big enough to cause problems with the structure of W - but modelling Y by using W and X was possible - no errors ! In a normal log-file, after the selection of the restraints, the SPLINE_RANGE is set; might a change in parameters help, or are there simply to many restraints (using 1*W and 3*Y produces only 25000 restraints, not 68000) ? I tried several other third templates, such as pdb-files that were produced by Modeller4 in previous sessions and that are structurally very close to Y, but then I get the error addcc2_E> too many parameters, increase MPRMCNS . I am grateful for any help you can offer me to solve this problem. Thank you very much in advance, Thorsten Schweikardt

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09 Dec '98

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What's the best way to deal with DNA?
by Daniel John Rigden 08 Dec '98

08 Dec '98

Hi modellers I want to build a model of a protein-DNA complex. I'd like to include the DNA somehow in Modeller's calculations so that the side chains of DNA-ligating residues don't overlap with the DNA; it doesn't need to be any more detailed than that. >From the manual and __homcsr.top, if I understand correctly, the presence of DNA as either HETATM or as BLK residues would produce some distance restraints that would help stop the protein overlapping the DNA. The problem is that I can't get the program to read in either HETATM or BLK residues. As I understand it, it should be necessary just to say SET HETATM_IO ON for HETATMs to be read in. However, even when I include this, and with the actual atoms in the pdb file in any number of formats (before/after the protein, with/without chain terminators), there are never any HETATMs selected. When the program reaches the hetatm_restraints subroutine I get ------------------------------------------------------------------------ TOP______> 191 167 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'HET' Number of atoms to choose from, total : 1372 1372 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : HET Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 178 1: 178: Selection residue step (SELECTION_STEP) : 1 selatm___> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RNUM AA --- RNUM AA LEN ------------------------------------------------------------------------ Likewise, when I define the DNA as BLK residues e.g. ATOM 1123 P BLK D 17 144.632 59.838 30.258 1.00 27.98 ATOM 1124 O1P BLK D 17 145.093 59.652 31.638 1.00 27.57 ATOM 1125 O2P BLK D 17 144.499 58.295 29.675 1.00 28.96 ATOM 1126 O5* BLK D 17 144.790 60.781 29.234 1.00 26.16 ATOM 1127 C5* BLK D 17 144.578 60.298 27.868 1.00 25.22 ATOM 1128 C4* BLK D 17 144.388 61.601 27.149 1.00 24.34 ATOM 1129 O4* BLK D 17 143.191 62.224 27.722 1.00 24.36 ATOM 1130 C3* BLK D 17 145.497 62.594 27.338 1.00 24.62 ATOM 1131 O3* BLK D 17 145.740 63.280 26.082 1.00 26.54 ATOM 1132 C2* BLK D 17 144.928 63.498 28.477 1.00 23.75 ATOM 1133 C1* BLK D 17 143.473 63.562 28.036 1.00 22.08 ATOM 1134 N9 BLK D 17 142.569 64.122 29.049 1.00 21.02 ATOM 1135 C8 BLK D 17 142.641 64.249 30.366 1.00 19.45 ATOM 1136 N7 BLK D 17 141.558 64.720 30.956 1.00 19.95 ATOM 1137 C5 BLK D 17 140.778 65.088 29.838 1.00 20.06 ATOM 1138 C6 BLK D 17 139.544 65.807 29.768 1.00 18.89 ATOM 1139 O6 BLK D 17 138.950 66.253 30.736 1.00 18.64 ATOM 1140 N1 BLK D 17 139.135 66.022 28.510 1.00 18.84 ATOM 1141 C2 BLK D 17 139.783 65.638 27.382 1.00 18.86 ATOM 1142 N2 BLK D 17 139.238 65.889 26.180 1.00 18.54 ATOM 1143 N3 BLK D 17 140.930 64.925 27.382 1.00 19.84 ATOM 1144 C4 BLK D 17 141.387 64.761 28.668 1.00 19.99 using an alignment file like >P1;2bop_dimer_DNAblk structureX:2bop_dimer_DNAblk: 326:A: 17:D: ---SCFALISGT-ANQVKCYRFRVKKNHRHRYENCTTTWFTVADNGAERQGQAQILITFGSP--SQRQDFLK HVPLPPGMNISG-FTASLDF/ ---SCFALISGT-ANQVKCYRFRVKKNHRHRYENCTTTWFTVADNGAERQGQAQILITFGSP--SQRQDFLK HVPLPPGMNISG-FTASLDF/ ................./ .................* the BLK residues are not read in and the blk_restraints subroutine finds no atoms to restrain. What am I doing wrong? Thanks a lot in advance Daniel Rigden

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modeller_usage