February 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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Re: HETATM
by Tony Pemberton 17 Feb '99

17 Feb '99

Dear Users, Thanks to all who contributed to solving this problem for me. I now have my HETATM (Zn) included in my output model. Andras Fiser's solution worked best, which was posted to this BBS. Regards, Tony Pemberton ********************************************************************* Mr. A.J.Pemberton Tel: +121-414-3388 c/o Dept. Rheumatology, Fax: +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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Re: [Fwd: HETATM (fwd)]
by Andras Fiser 16 Feb '99

16 Feb '99

Dear Tony, We got your files with the problem described below. Your Modeller run did not give you not only the hetatm but any output since it reported an error in the *.log file. It was complaining about the alignment. This is the most usual problem, users must pay attention to it. The log file clearly says, that there is a discrepancy in the number of residues among the seq.s and the pdb files: the number of residues are different in all cases. there are several problems: 1., you forgot to indicate in the header of each pir format alignmnet seq. that the number of residues is one resides longer, since you wanted to include a heteroatom as well. (e.g. see below ,instead of 500 you need 501) 2., Modeller learns from the pdb templates what kind of atom or residue to be read in: you indicated in the sequence that there is a "zn" hetatm, which is misleading. In the pir format you have single letter codes: Modeller thought you have 2 additional residues, a "z" and an "n". You need only to put "." to show that something else to be read in from the pdb files at that position. If you wants to have specificly Zn than you a., have to put "z" in the sequence, and b., ZN2 in the PDB files. The CHARMM atom types are listed in $MODINSTALL/modlib/restyp.lib. Modeller clearly complained that you have too many residues in the sequences (in all of them) i.e. z, n, and "." as well for a single hetatm. i.e. e.g.: original: >P1;1glu_B structureX:1glu_znf_b: 458: B : 500: B: Glucocorticoid Receptor: : : GSCKVFFKRAVEGQ-HNYLCAGRNDCIIDKIRRKN-------CPACRY-RKC/.zn* correct: >P1;1glu_B structureX:1glu_znf_b: 458: B : 501: B: Glucocorticoid Receptor: : : GSCKVFFKRAVEGQ-HNYLCAGRNDCIIDKIRRKN-------CPACRY-RKC/z* the corrected alignment file with your top script now produces structures to me, though you need figure out additional marginal problems. e.g. your templates at certain positions are too different etc. good luck for the future, andras > > > > > > A.J.Pemberton wrote, > > > > > > > Dear users, > > > > > > > >I have set my steering file to activate the HETATM usage (modeller 4): > > > > > > > >SET TOPOLOGY_MODEL = 1, HETATM_IO = on, HYDROGEN_IO = on, WATER_IO = on > > > > > > > >as per FAQ question 15 > > > > > > > >but modeller is not giving me HETATMs is the pdb output, why? > > > > > > > >Regards, > > > > > > > >Tony > > > > > > > >********************************************************************* > > > >Mr. A.J.Pemberton Tel: +121-414-3388 > > > >c/o Dept. Rheumatology, Fax: +121-414-3982 > > > >Medical School, E-mail: A.J.Pemberton(a)bham.ac.uk > > > >The University of Birmingham, > > > >Birmingham B15 2TT. > > > >U.K. > > > >********************************************************************* > > > > > > > > > I have the same problem !!! > > > > > > > > > Antonello Romani > > > > > > > > > > > > > > > ___________________________________________________________________________ > > > Antonello Romani > > > Istituto di Patologia Generale > > > Plesso Biotecnologico Integrato > > > Facolta' di Medicina e Chirurgia > > > Universita' degli Studi di Parma > > > via Volturno 39 > > > 43100 Parma > > > > > > Tel: +39 0521 903 764 > > > Fax :+39 0521 903 742 > > > > > > E-Mail : A.Romani(a)leonardo.biomed.unipr.it > > > > > > > > > ___________________________________________________________________________ -- , Andras Fiser, PhD # phone: (212) 327 7206 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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Re: HETATM
by Derek Smith 15 Feb '99

15 Feb '99

Dear Tony and Antonello, I too had the problem of not getting heteroatoms in my models when I had specified HETATM_IO = on. I sorted it out as follows... 1. Is the HETATM already parameterised in MODELER? if so... 2. Have you specified the HETATM in the alignment file? I use MODELER through QUANTA, which puts heteroatoms into the PDB input files but doesn't automatically put heteroatoms into the sequence alignment, so I have to edit the file manually. 3. Have you aligned the HETATMs for template and model sequence? If the hetatm for template and model sequence are not equivalent then your hetatm occurs in the postion of what would be the next C-alpha atom in your chain. It's very basic I know - but sometimes mistakes can happen. I hope it works out for you both. Derek.

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HETATM
by A.Romani＠leonardo.biomed.unipr.it 15 Feb '99

15 Feb '99

-------- A.J.Pemberton wrote, > Dear users, > >I have set my steering file to activate the HETATM usage (modeller 4): > >SET TOPOLOGY_MODEL = 1, HETATM_IO = on, HYDROGEN_IO = on, WATER_IO = on > >as per FAQ question 15 > >but modeller is not giving me HETATMs is the pdb output, why? > >Regards, > >Tony > >********************************************************************* >Mr. A.J.Pemberton Tel: +121-414-3388 >c/o Dept. Rheumatology, Fax: +121-414-3982 >Medical School, E-mail: A.J.Pemberton(a)bham.ac.uk >The University of Birmingham, >Birmingham B15 2TT. >U.K. >********************************************************************* I have the same problem !!! Antonello Romani ___________________________________________________________________________ Antonello Romani Istituto di Patologia Generale Plesso Biotecnologico Integrato Facolta' di Medicina e Chirurgia Universita' degli Studi di Parma via Volturno 39 43100 Parma Tel: +39 0521 903 764 Fax :+39 0521 903 742 E-Mail : A.Romani(a)leonardo.biomed.unipr.it ___________________________________________________________________________

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HETATMs
by Tony Pemberton 15 Feb '99

15 Feb '99

Dear users, I have set my steering file to activate the HETATM usage (modeller 4): SET TOPOLOGY_MODEL = 1, HETATM_IO = on, HYDROGEN_IO = on, WATER_IO = on as per FAQ question 15 but modeller is not giving me HETATMs is the pdb output, why? Regards, Tony ********************************************************************* Mr. A.J.Pemberton Tel: +121-414-3388 c/o Dept. Rheumatology, Fax: +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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SEQUENCE_COMPARISON: wrong calculation for variability
by Timothy A. Springer Ph.D. 14 Feb '99

14 Feb '99

I like the sequence comparison functions in Modeller. I would like to calculate sequence conservation or variabilty as a function of position. One of the proteins I work with contains a conserved domain, and I would like to plot this. Unfortunately, variability as a function of alignment position is not calculated in a meaningful way. It does calculate what it says it calculates, but the result is not helpful at all - it is the RMS deviation of all residue - residue scores. I have plotted this, and it shows little relationship to highly conserved areas. It picks up positions of identity fine, but that is about it. Could you please implement a calculation of sequence conservation. I suggest the total of the similarity scores. You could divide this by the maximal number of sequence comparisons. I would not divide by the number of comparisons at each position, because this may be small for positions with gaps, and might overestimate conservation in gapped regions. Also, the documentation says gaps are included in the scoring matrix, but this is only true for the blosum matrix. Thanks, Tim Springer >From the manual: SEQUENCE_COMPARISON -- compare sequences in alignment Description: The family variability as a function of alignment position is calculated as the RMS deviation of all residue - residue scores at a given position, but only for those alignment positions that have at most MAX_GAPS_MATCH gaps. The variability is written to file VARIABILITY_FILE , as is the number of pairwise comparisons contributing to each positional variability. ******************************************************************************* * Timothy A. Springer, Ph.D. * * Latham Family Professor of Pathology * * Harvard Medical School e-mail: springer(a)sprsgi.med.harvard.edu * * Center for Blood Research phone: 617-278-3200 * * 200 Longwood Ave. Room 251 fax: 617-278-3232 * * Boston MA 02115 * *******************************************************************************

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Re: Refinement from my own initial Structure
by Tony Pemberton 12 Feb '99

12 Feb '99

On 28th Jan, I wrote:- 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. THE SOLUTION ------------ After reading through the modeller steering files and constructing a flow chart of the procedure, I realised that I was essentially correct about the BUILD_METHOD being a "flag". This acts as a variable but it is the *wrong* variable. It should be GENERATE_METHOD not BUILD_METHOD Therefore the line in the above script should read: SET MODEL = 'ref.old', GENERATE_METHOD = 'read_xyz' This variable is evaluted in __homcsr.top in the 'homcsr' subroutine. The default is 'transfer_xyz' 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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sequence_to_ali command
by modelisation 09 Feb '99

09 Feb '99

Dears, we have an unexplained problem when using the SEQUENCE_TO_ALI command: only the first residue of the MODEL (template) file is transfered to the alignment array, e.g if we write an alignment file, only the first residue appears, though the right number of residues is written by the program (the second line of the alignment file includes the first and last residue number of my pdb file). Here is an example of the output i get when try to test this command on 5fd1: >P1;all structureX:all: 1 : : 106 : :undefined:undefined:-1.00:-1.00 A* I would like to precise that we get this problem when using the example loop routine, as well as when simply testing the command e.g: READ_MODEL FILE = '5fd1.ent' SEQUENCE_TO_ALI WRITE_ALIGNMENT FILE='5fd1.ali' What did we do wrong? Regards. Michel Giorgi Lab. Cristallochimie Fac. St. Jerome, Marseille, France

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Copper parametrization
by Michel Giorgi 05 Feb '99

05 Feb '99

Hi! After some difficult startings with the MODELLER package i feel now really enthusiastic about the possibilities of the program. Anyway i have a question: did one of you parametrized the copper atom? i.e do you know the radii values we have to enter in the radixx.lib files and the nonbonded constants of the parm.lib file? (what is the meening of these last values?) Maybe as a first (good?) approximation i could use the values of the ZN atom which is parametrized. Anyone has an idea? Regards, -- Michel GIORGI Lab. de Cristallochimie Faculte de St. Jerome Marseille, cedex 20, FRANCE

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