modeller_usage

modeller_usage@salilab.org

4 participants
3146 discussions

modelling
by Prof. Zafar H. Zaidi 27 Jul '98

27 Jul '98

I am trying to model a tetramer. The number of residues in the target protein are 141 each in 2 subunits and 146 each in the other two. The target is single, also a tetramer with the same number of amino acids in the four subunits. Following is the format of the alignment file: C; alignment in the PIR format >P1;----- structureX:-----:1:A:146:D:name:source:: ------------------------------------------------------------------------- ---------------------------------------------/ ------------------------------------------------------------------------- ---------------------------------------------/ ------------------------------------------------------------------------- ---------------------------------------------/ ------------------------------------------------------------------------- ---------------------------------------------* >P1;----- sequence:-----:1:A:146:D:name:source:: ------------------------------------------------------------------------- ---------------------------------------------/ ------------------------------------------------------------------------- ---------------------------------------------/ ------------------------------------------------------------------------- ---------------------------------------------/ ------------------------------------------------------------------------- ---------------------------------------------* Please make sure that the above format is correct. Moreover the total number of residues amounts to above 1000 which is more than the specified limit. Please suggest the solution. Thanks

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Building loops in Modeller
by Robert Jorissen 13 Jul '98

13 Jul '98

Dear fellow Modeller users I am using Modeller 4 to build a comparative model and am at the stage of constructing loops. Do I accept the loop with the lowest score (as long as it is plausible) or do I use other criteria as well e.g. combination of low score and favourable ProsaII plot over the region of the loop. Rob -- ----------------------------------------------------- Robert Jorissen Ludwig Institute for Cancer Research P.O. BOX 2008, Royal Melbourne Hospital Parkville, Victoria 3050, Australia phone: ++61-3-9341-3155 fax: ++61-3-9341-1938 e-mail: Robert.Jorissen(a)ludwig.edu.au -----------------------------------------------------

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precision of compilation
by Jiri Damborsky 09 Jul '98

09 Jul '98

Dear Modeller users; I have been using Modeller v. 3c for some time and more recently started to use v. 4h for my modelling projects. However, version 4 seems to give worse results with regards to stereochemical quality (e.g., checked by PROCHECK). I used the same top.file for both versions but the results were different. Very recently I found out, that my v. 4h is compiled with single precision, while v. 3c is compiled with double precision. Could this be the reason for difference in quality of results? Is the version 4 available with double precision? Thank you for your reply. Best wishes, Jiri * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Dr. Jiri Damborsky Laboratory of Biomolecular Structure & Dynamics Masaryk University Kotlarska 2 611 37 Brno Czech Republic e-mail: jiri(a)chemi.muni.cz phone: +420-5-41129 377 FAX: +420-5-41129 506 http://web.chemi.muni.cz/~jiri

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Re: Creating new residue types
by Andrej Sali 09 Jul '98

09 Jul '98

Another note on new residue types: Version 5 of modeller, to be released by the end of August, is compatible with the QUANTA RTF editor. So the easiest way to generate a new RTF entry would be to use QUANTA's RTF editor, write it out, and include it in the MODELLER lib file. Also, we will have many more molecules/residues in the standard MODELLER RTF library to begin with. I know, not everybody has access to QUANTA ... Best, Andrej -- 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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Creating new residue types
by Christian Barrett 09 Jul '98

09 Jul '98

Hello Modeller users, I am building a homology model from a template that contains hetero atoms that I don't want to include as block (BLK) residues. This means that they must exist in the residue type library (modlib/restyp.lib). Before I attempt to create two new library entries, I would like to know if somebody has already done this for the HETATM entries that I am interested in. They are FDP (FRUCTOSE-2,6-BISPHOSPHATE) and AMP (ADENOSINE MONOPHOSPHATE) Thanks, Christian Barrett

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Problem building multi-subunit proteins
by Thomas Blicher 09 Jul '98

09 Jul '98

Dear Modellers. I am trying to model MHC class I molecules and have come across a problem which appears to be related to the alignment. MHC molecules consist of three individual peptide chains and I have therefore specified my input sequence in the alignment file with the chain break character / (see alignment file below). When modelled, this gives rise to a model with a serious flaw: It appears that the chain break character is interpreted by MODELLER as a kind of "dummy residue". The result is that the first chain is modelled nicely, but the second and third chains are shifted by one and two residues, respectively. This is a BIG problem, especially as I am interested in the exact interactions of the third chain (a small oligopeptide) with the rest of the molecule. I have come up with a temporary "solution" (hopefully) where I simply delete the last residue of the first and second chain in order to make room for the "dummy residue". This produces nice models (which are lacking two residues), but I would like to be able to model the entire molecule. This is my alignment file which is modelled by the model.top routine: >P1;1hhi structureX:1hhi: 1:A : 9:C : MHC I: HLA-A0201: * >P1;1A11 sequence:1A11: 1:A : @:@ : MHC I: HLA-A1101: GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAP WIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYG CDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAA HAAEQQRAYLEGRCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEAT LRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVP SGEEQRYTCHVQHEGLPKPLTLRWE/ MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKV EHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM /GILGFVFTK * I've probably forgotten something essential, but I don't see what it is. I would be happy for any comments and suggestions. Many thanks. Thomas --------------------------------------------------------------------------- Thomas Blicher, Department of Chemistry, Universitetsparken 5, Copenhagen University, 2100 Copenhagen Denmark. phone: 45-35320280, fax: 45-35320299 E-mail: thomas(a)kage.ki.ku.dk

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Calciums and disulphides
by Derek Smith 28 Jun '98

28 Jun '98

Dear Modellers I am trying to model some proteins with a calcium binding site. Looking in the manual, I altered my sequence alignment as so: FIRST-TEMPLATE--/3* SECOND-TEMPLATE-/3* THIRD-TEMPLATE SEQUENCE--------/3* When I try to model the sequence, I end up with the calcium in the position of the next (and non-existent) c-terminal residue. Can anyone help with this? Have I used incorrect notation for the sequences? Also, another project I'm attempting involves adding two disulphide restraits to a model. If I model the protein without the restraints, PATCH_DISULFIDES finds three disulfides, and I end up with a refined model with an objective function of ~800. When adding the special patches, I get an unrefined model with an objective function of ~109000. The structural alignment suggests that at least one of the cysteine pairs are in the right positions for disulphide formation, yet just adding that restraint gives the same result (huge objective function). Do you have any suggestions? Yours, Derek. -- ************************************************************************ Derek Smith email: derek(a)yorvic.york.ac.uk Department of Chemistry University of York, Heslington, York. YO1 5DD United Kingdom. ************************************************************************

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Query,
by Dr P.A. Reche 23 Jun '98

23 Jun '98

Hi there, I have a few questions about using modeller. I have been trying to use the MALIGN routine of the Modeller package and I have got a few problems. Firstly, I am limited to use just five sequences and I would like to know how to increase the number of sequences that the program can handle. Secondly, I am having some problems runing this routine since I guess that the primary homology between my structures is very low. Actually, the program runs till this point: chkseq__E> sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 4 1 0 #### 12 ASN ----------- 4 2 0 #### 3 ASP ----------- 4 3 0 #### 20 TYR ----------- 4 4 0 #### 5 PHE ----------- 4 5 0 #### 15 ARG ----------- 4 6 0 #### 1 ALA ----------- 4 7 0 #### 3 ASP ----------- 4 8 0 #### 16 SER ----------- 4 9 0 #### 15 ARG ----------- 4 10 0 #### 17 THR ----------- fit2xyz_E> number of equivalent positions < 3: 0 recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1 Will you please tell what is going on. Also, I have a general question. Is it possible to superimpose a set of structures at once (not one to one)? and finally is it possible to use MALIGN3D without feeding in the script an initial alignment? Thanks a lot. Pedro Reche ============================================================================== Dr. Pedro Antonio Reche Gallardo Dept. of Biochemistry, U. of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, England, UK Phone: +44 (0)1223 333662 Fax: +44 (0)1223 333661 par(a)mole.bio.cam.ac.uk http://www-ccmr-nmr.bioc.cam.ac.uk/~par

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Problem building 2-domain protein
by Pieter Stouten 23 Jun '98

23 Jun '98

We have a problem building a 2-domain protein based on multiple (8) other proteins. We put a slash between the two domains so that Modeller knows not to connect the termini. We have no problems with large distances between equivalent CA's of different proteins. the only unusual aspect we notice is that the pair of warnings (?) "drmsq1__W> n<2 and drmsq3__W> n<2" occurs 19 times. No error message occurs, but no model is produced either. Please find attached part of the output. Hope this is enough for the experts on ths list to give us hints as to how to resolve this issue. Thanks a million, Pieter Stouten <pieter.stouten(a)dupontmerck.com> DuPont Merck - Computer Aided Drug Design Group Web: http://www.halcyon.com/stouten/ ---------------------------------------------------------------------------- chkaln___> Checking pairwise structural superpositions: Equivalent CA pairs with distance difference larger than 6.0 angstroms: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- drmsq1__W> n<2 drmsq3__W> n<2 [... repeated 19 times ... /PFWS] chkaln___> Checking structure-sequence alignments: Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- << end of CHECK_ALIGNMENT. TOP______> 109 94 CALL ROUTINE = BUILD_METHOD TOP______> 110 66 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS [...] TOP______> 111 67 MALIGN3D FIT = OFF, GAP_PENALTIES_3D = 0 4 malign3d_> Initial framework positions: 9 fit2xyz_E> number of equivalent positions < 3: 0 recover__> MODELLER_STATUS >= CONTROL: 1 1

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model building with symmetry
by Jean-Luc Ferrer 23 Jun '98

23 Jun '98

Hye, I would like to build a model for a dimere (the 2 molecules are 2-fold axis symmetry related). I tried to duplicate the sequence of the monomere, separated by a /: >P1;acs sequence:acs:. :.:. :.:?: : 3.66: 0.00 MESLKEMRKAQMSEGPAAILAIGTATPDNVFMQADYPDYYFRMTKSEHMTELKDKFRTLCEKSMIRKRHMCFSED FLKANPEVCKHMGKSLNARQDIAVVETPRLGNEAALKAIKEWGQPKSSITHLIFCSSAGVDMPGADYQLTRILGL NPSVKRMMIYQQGCYAGGTVVRLAKDLAENNKGSRVLVVCSELTAPTFRGPSPDAVDSLVGQALFADGAAALVVG ADPDSSIERALYYLVSASQMLLPDSDGAIEGHIREEGLTVHLKKDVPALFSANIDTPLVEAFKPLGISDWNSIFW IAHPGGPAILDQIEEKLGLKEDKLRASKHVMSEYGNMSSSCVLFVLDEMRSRSLQDGKSTTGQGLDWGVLFGFGP GLTVETIVLRSVPIEA/ MESLKEMRKAQMSEGPAAILAIGTATPDNVFMQADYPDYYFRMTKSEHMTELKDKFRTLCEKSMIRKRHMCFSED FLKANPEVCKHMGKSLNARQDIAVVETPRLGNEAALKAIKEWGQPKSSITHLIFCSSAGVDMPGADYQLTRILGL NPSVKRMMIYQQGCYAGGTVVRLAKDLAENNKGSRVLVVCSELTAPTFRGPSPDAVDSLVGQALFADGAAALVVG ADPDSSIERALYYLVSASQMLLPDSDGAIEGHIREEGLTVHLKKDVPALFSANIDTPLVEAFKPLGISDWNSIFW IAHPGGPAILDQIEEKLGLKEDKLRASKHVMSEYGNMSSSCVLFVLDEMRSRSLQDGKSTTGQGLDWGVLFGFGP GLTVETIVLRSVPIEA* and create a known structure for each monomere of the template: >P1;chs1 structureX:chs1: 1 : : 389 : :chalcone synthase: : 1.80: 0.00 MVSVSEIRKAQRAEGPATILAIGTANPANCVEQSTYPDFYFKITNSEHKTELKEKFQRMCDKSMIKRRYMYLTEE ILKENPNVCEYMAPSLDARQDMVVVEVPRLGKEAAVKAIKEWGQPKSKITHLIVCTTSGVDMPGADYQLTKLLGL RPYVKRYMMYQQGCFAGGTVLRLAKDLAENNKGARVLVVCSEVTAVTFRGPSDTHLDSLVGQALFGDGAAALIVG SDPVPEIEKPIFEMVWTAQTIAPDSEGAIDGHLREAGLTFHLLKDVPGIVSKNITKALVEAFEPLGISDYNSIFW IAHPGGPAILDQVEQKLALKPEKMNATREVLSEYGNMSSACVLFILDEMRKKSTQNGLKTTGEGLEWGVLFGFGP GLTIETVVLRSVAI--/ --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------* >P1;chs2 structureX:chs2: 1 : : 389 : :chalcone synthase: : 1.80: 0.00 --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------/ MVSVSEIRKAQRAEGPATILAIGTANPANCVEQSTYPDFYFKITNSEHKTELKEKFQRMCDKSMIKRRYMYLTEE ILKENPNVCEYMAPSLDARQDMVVVEVPRLGKEAAVKAIKEWGQPKSKITHLIVCTTSGVDMPGADYQLTKLLGL RPYVKRYMMYQQGCFAGGTVLRLAKDLAENNKGARVLVVCSEVTAVTFRGPSDTHLDSLVGQALFGDGAAALIVG SDPVPEIEKPIFEMVWTAQTIAPDSEGAIDGHLREAGLTFHLLKDVPGIVSKNITKALVEAFEPLGISDYNSIFW IAHPGGPAILDQVEQKLALKPEKMNATREVLSEYGNMSSACVLFILDEMRKKSTQNGLKTTGEGLEWGVLFGFGP GLTIETVVLRSVAI--* and run the model.top script: > INCLUDE # Include the predefined TOP routines > SET ALNFILE = 'acs.align' # alignment filename > SET KNOWNS = 'chs1' 'chs2' # codes of the templates > SET SEQUENCE = 'acs' # code of the target > SET ATOM_FILES_DIRECTORY = '../../pdb/' # directories for input atom files > SET STARTING_MODEL= 1 # index of the first model > SET ENDING_MODEL = 1 # index of the last model > CALL ROUTINE = 'model' # do homology modelling and then I get the error: > chkaln___> Checking pairwise structural superpositions: > Equivalent CA pairs with distance difference larger than 6.0 angstroms: > > ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST > ---------------------------------------------------- > drmsq1__W> n<2 > drmsq3__W> n<2 > > chkaln___> Checking structure-sequence alignments: > Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: > > ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST > ---------------------------------------------- > > > << end of CHECK_ALIGNMENT. fit2xyz_E> number of equivalent positions < 3: 0 recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1 I guess it certainly not the right way to do that. So, if somebody has any suggestion... Thanks Jean-Luc ------------------------------------ Jean-Luc FERRER Structural Biology Laboratory The Salk Institute for Biol. Studies P.O. Box 85800 San Diego, California 92186-5800 USA phone: (619) 453-4100 ext 1535/1383 fax: (619) 452-3683 email: ferrer(a)lccp.ibs.fr ------------------------------------

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modeller_usage