- modeller_usage - salilab.org

bus error
by mdatt＠imtech.res.in 12 May '05

12 May '05

hi all on doing comparative modelling using modeller v8 i got bus error. here i'm attaching my input files thanks for any help Manish Datt

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(no subject)
by Manish Datt 11 May '05

11 May '05

hi all i`ve recently installed modeller v8 on sgi irix machine. when in tried to perform comparative modeling, using the script given in examples, i got bus error. also there was warning: ulimit exceed allowable limits. on checking i discovered that ulimit has been set to unlimited. any help would be highly appreciated. regards, Mansih Datt Research Fellow Bioinformatics Centre IMTECH Chandigarh, India.

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tetramers in symmetry
by hchoe 09 May '05

09 May '05

Dear Modellers, I have used the following subroutine to define tetramers in symmetry. Please tell me how to do it in MODELLER8v0. SUBROUTINE ROUTINE = 'defsym' SET RES_TYPES = 'ALL', ATOM_TYPES = 'MNCH', SELECTION_STATUS = 'INITIALIZE', SELECTION_SEARCH = 'SEGMENT', SYMMETRY_WEIGHT = 1.0 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '37:' '322:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '323:' '608:' DEFINE_SYMMETRY ADD_SYMMETRY = on off PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '323:' '608:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '609:' '894:' DEFINE_SYMMETRY ADD_SYMMETRY = on off PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '609:' '894:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '895:' '1180:' DEFINE_SYMMETRY ADD_SYMMETRY = on off PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '895:' '1180:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '37:' '322:' DEFINE_SYMMETRY ADD_SYMMETRY = on off RETURN END_SUBROUTINE Thanks in advance. Cheers, Han

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heteroatom
by arul prakasam 08 May '05

08 May '05

dear sir iam modeling a model which has heteroatom FE2 at its active site my template and target has FE2 what should i do to model this ________________________________________________________________________ Yahoo! India Matrimony: Find your life partner online Go to: http://yahoo.shaadi.com/india-matrimony

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model refinement and assessment
by Stephen A. Smith 28 Apr '05

28 Apr '05

Hi In MODELLER 7v7 one was able to turn off model refinement using: SET MD_LEVEL = 'nothing' I am curious if there is an analogous way to do this in 8v0? I've looked through the manual and examples and have not found a solution. Have I missed something simple? Is there a way to implement the GA341 and DOPE methods of analysis during the same model building session? I'm also interested in using these analysis methods on other protein models and templates. Is there a quick way to read these models into MODELLER and let it analyze them? Thank you Steve __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Loops
by John Penniston 27 Apr '05

27 Apr '05

When I attempt to optimize a portion of a molecule for which I don't have a good homolog, the loop optimization procedure always yields a rather nondescript coil with no sheet or helix. Today I tried, as an exercise, to see what "optimization" did to a known crystal structure. I ran the program on the C-terminal helix of calmodulin, a molecule for which the structure is very well known. As has been my experience before, the result was destruction of that nice orderly helix, which was replaced by a coil going off in no particular direction. Can anyone tell me why this happens, and how I can use this procedure to get a better result? Thanks. John Penniston

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MODELER v6.3 script
by O'MAHONY, BRIAN 27 Apr '05

27 Apr '05

I am trying to refine a loop region in my protein using "select atoms". The roblem is I only have the manual for version 4 and many variables have been redefined. Can someone tell me the script or better still send me the manual for version 6.3. I can't find it on the net Brian O'Mahony Institut Municipal de Investigació Mèdica (IMIM) Pharmacology Research Unit Dr. Aiguader, 80 E-08003 Barcelona, Spain Tel: +34 - 93 225 25 97 E-mail: mailto:bomahony@imim.es Web: http//www.imim.es

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Multidomain protein
by Ranjit Kumar 25 Apr '05

25 Apr '05

Dear Sir, I am trying to model a protein which has three domains seperated by linker region in a linear fashion.Domain are not overlapping as they are seperated by linkers.By macromolecular docking I generated their best possible orientation and used as input PDB files.But the model given by modeller wont preserve the provided orientation and domain got seperated further by the linker regions.The template for linker region has streches of helixes seperated by coils. So what should I do to preserve the domain orientation and then generate the possible model or I should use any other approach? Waiting for your reply.... Research Student Ranjit Kumar

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An error with final_malign3d
by Mensur Dlakic 25 Apr '05

25 Apr '05

Hi, This error occurs both with Windows and Linus versions of Modeller 8v0 when 'a.final_malign3d = True' is left in the script file. If this statement is commented out and the script is otherwise unchanged, it works just fine. The job gets stopped right at the very end, presumably before the models are fitted to the template. Similar thing happens when these two lines are in the script: mdl = model(env) mdl.optimize(optimization_method=3, max_iterations=50, output='REPORT', trace_output=1) In this case, however, the script dies at the beginning. Again, commenting out these two statements is all it takes to get the job going. I'll send the error messages to Ben only, the whole list probably doesn't need to see them. Any suggestion/advice is appreciated. Cheers, Mensur ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic(a)montana.edu | ==========================================================================

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pick.atoms
by jean-marc vuissoz 25 Apr '05

25 Apr '05

hello, I would like to do a selection of many atoms ( 45-46, 110-112, 147-149), but I don't manage to do it, how should I dot it ? best tanks jean-marc # select_loop_atoms (necessary) class myloop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # 4 residue insertion (1st loop) self.pick_atoms(selection_segment=('147:', '149:'), selection_status='INITIALIZE')

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