- modeller_usage - salilab.org

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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Optimizing Models
by DEBASHIS MUKHOPADHYAY 22 Jun '98

22 Jun '98

Dear Modellers, It appears that I have successfully modelled a mutated protein using 'model.top' routine which generated 20 output co-ordinates to choose from. It is noted that each file contains a parameter called MODELLER OBJECTIVE FUNCTION - most possibly indicating the model quality(?). Now, the question is which value of the function to consider - the lowest one or vice versa? Also, when I checked the secondary str. etc. of one such model using PROCHECK, several bad contacts were noted. Can you suggest any particular 'top' routine which will eventually eliminate all these / or optimize them, so as to make the model acceptable? Thanks in advance. Debashis

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model building questions
by Christian Barrett 09 Jun '98

09 Jun '98

Hi there. I have been able to perform the basics of building a homology model and have a few questions about improving it. I built the model with the top script below: ------------------------------------------------------------------------- INCLUDE # Include the predefined TOP routines SET ALNFILE = '1frp+1fbp+Prgn.ali' # alignment filename SET KNOWNS = '1frpA 1fbpA' # codes of the templates SET SEQUENCE = 'Prgn' # code of the target SET ATOM_FILES_DIRECTORY = '.' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) SET HETATM_IO = 'on' CALL ROUTINE = 'model' # do homology modelling ------------------------------------------------------------------------ The structures 1frpA and 1fbpA are the same, and they contain hetero atoms. I haven't been able to use the hetero atoms as restraints and transfer them to the homology model using BLK or "." Can I do this with a slight modification to this script? What exactly is the meaning behind setting "STARTING_MODEL" and "ENDING_MODEL"? Does setting the former to 1 and the latter to, say, 7 result in seven models being built with the 7th model being the most refined? I'm not clear on how to refine a model. Without providing any other constraints other than what is provided by the structures and hetero atoms, is this straightforward to do by augmenting the above script? Thanks, Christian Barrett

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Info on V999??? files
by aldo jongejan 05 Jun '98

05 Jun '98

Hi, A question from a beginner: I would like to know what the information in the V999??? files means and how its is correlated to the information given in the .log files. It seams to me that the tables in the V999??? files does not completely correspond to the 31 classes of the restraint violations table in the .log file. Is there a difference in the order of columns?? Fx. there is a zero for the LJ 6-12 potential, but in the V999?? file there are some numbers. The zero-values in the table are not matched by the empty columns in the V999?? files. thanks for any help, aldo __________________________________________________________ aldo jongejan Kluyver Laboratorium for Biotechnology Technical University of Delft Julianalaan 67 tlf: +31 (0)15 2782336 2628 BC Delft fax: +31 (0)15 2782355 The Netherlands e-mail: aldo(a)dutsh15.tudelft.nl __________________________________________________________

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dismiss. this is a test
by Azat Badretdinov 04 Jun '98

04 Jun '98

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two questions
by Christian Barrett 12 May '98

12 May '98

Hi, I've recently built a homology model and have two questions that I can't find answers to in the documentation. Question 1: My template structure has hetero atoms in it. Can I 1) make these carry over into the homology model and 2) use them as restraints in building the homology model. (The hetero atoms are in contact with the template structure just as I expect them to be with the homology model. I would like this to be realized in the homology model.) Question 2: This is more a request for advice on analyzing my homology model. What is the best way to see if it makes sense? For instance, I would like to know if the core is suspiciously populated with energetically unfavorable residues, if one face of the protein is too hydrophobic, implying that it ought to be in hydrophobic contact with (in my case) the other half of the protein for which I cannot built a homology model, etc. I could do something like color hydrophobics and hydrophilics different colors and visually inspect the model, but I'm interested in something a little bit more convincing and principled. What would you do to convince yourself that the protein could be physically realizable? Thanks for any suggestions, Christian Barrett

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Energy minimization
by zaidi＠prochem.khi.sdnpk.undp.org 06 May '98

06 May '98

Hi Andrej We have docked a small peptide on the active site of protease molecule, now want to perform structural refinement and energy minimization. Can OPTIMIZE command of modeller do that or implementation of any energy minimizer is needed. Kindly note, OPTIMIZE successfully eliminate all short non-bonded contacts and improved stereochemical parameters of the initial enz-inhibitor complex.. Secondly, is it obligatory to use minimizer during these type of work. Advise please. Regards Kamran Azim

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