December 1998 - 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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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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How to define symmetry?
by Daniel John Rigden 08 Dec '98

08 Dec '98

Dear Modellers I'm trying to build a dimer, constraining the two monomers to be identical. From the manual this seems reasonably straightforward but I can't get it to work. My current idea is to include the commands in the 'special_restraints' subroutine (in __special.top), which gets called by __homscr.top after the other restraints subroutines, thus SUBROUTINE ROUTINE = 'special_restraints' # Try to put symmetry restraints here # This is called from __homcsr after other restraints set up SET ATOM_TYPES = 'ALL' SET SELECTION_STATUS = 'INITIALIZE' SET SELECTION_SEARCH = 'SEGMENT' SET SYMMETRY_WEIGHT = 5.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '1:' '89:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '90:' '178:' DEFINE_SYMMETRY ADD_SYMMETRY = on off RETURN END_SUBROUTINE I know that this subroutine is read but I never see any indication of symmetry having been set up when I read the logfile. What am I doing wrong? Thanks in advance Daniel Rigden

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Modelling Hetero trimers
by Jeffrey P. Jones 07 Dec '98

07 Dec '98

I am trying to model a heterotrimeric protein with Modeller. How do I designate the different chains? My template molecule contains three chains, as does the model I'm trying to make. When I use Modeller I get a single chain which distorts my overall tertiary structure. Do I have to model each chain individually or am I missing something? Jeff Jeffrey P. Jones, Associate Professor of Chemistry Room 477 Fulmer Hall, Washington State University Pullman WA 99164-4630, jpj(a)wsu.edu http://cyp.chem.wsu.edu/~jpj/jones_group.html (509) 335-5983, Fax (509) 335-8867

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Change of jobs
by stouten＠nwnexus.com 06 Dec '98

06 Dec '98

Hello colleague/friend, As per December 1, 1998, I have taken up a position as head of computational chemistry with Pharmacia & Upjohn near Milano, Italy. Everything happened so fast that I did not have the opportunity to inform you of my relocation prior to my leaving DuPont Pharma. I apologize if mail that you sent to my old address the past two weeks bounced. I also apologize if you receive this mail more than once. Although my e-mail situation has not yet been completely resolved, please send work-related mail to: pieter.stouten(a)eu.pnu.com and private mail to: stouten(a)iname.com (preferred) or stouten(a)halcyon.com Although, the mail you are reading now may seem to come from stouten(a)nwnexus.com, please do *NOT* use that address to send me mail. Use one of the three listed above instead. If you happen to be a molecular modeller who is interested in joining a vibrant and rapidly expanding organization specialized in oncology research, please send me a mail. All the best, Pieter

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Change of jobs
by stouten＠nwnexus.com 06 Dec '98

06 Dec '98

Hello colleague/friend, As per December 1, 1998, I have taken up a position as head of computational chemistry with Pharmacia & Upjohn near Milano, Italy. Everything happened so fast that I did not have the opportunity to inform you of my relocation prior to my leaving DuPont Pharma. I apologize if mail that you sent to my old address the past two weeks bounced. I also apologize if you receive this mail more than once. Although my e-mail situation has not yet been completely resolved, please send work-related mail to: pieter.stouten(a)eu.pnu.com and private mail to: stouten(a)iname.com (preferred) or stouten(a)halcyon.com Although, the mail you are reading now may seem to come from stouten(a)nwnexus.com, please do *NOT* use that address to send me mail. Use one of the three listed above instead. If you happen to be a molecular modeller who is interested in joining a vibrant and rapidly expanding organization specialized in oncology research, please send me a mail. All the best, Pieter

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