- modeller_usage - salilab.org

Special Considerations in Membrane-bound models?
by Andrew D. Fant 10 Sep '07

10 Sep '07

Good morning, I'm looking at trying to build models of a set of membrane-bound proteins via structural homology, and I was wondering if there are any special caveats that apply to this situation. Thanks, Andy

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Model quality assessment
by saccenti＠cerm.unifi.it 10 Sep '07

10 Sep '07

Which is the best strategy to assess the quality of a model and sort them out of a bunch of many calculated models? I have models a complex of two proteins plus a metal ion. Many Thanks edo -- Dr Edoardo Saccenti CERM Magnetic Resonance Center University of Florence Fiorgen Foundation Via Luigi Sacconi n° 6 50019 Sesto Fiorentino (FI) Italy Tel: +39 055 4574281

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modeller.top location?
by DANIEL TAYLOR 07 Sep '07

07 Sep '07

Greetings Forum users I'm a final year Biochemistry undergraduate and am slowly learning the ropes when it comes to computers; I have recently installed modellerv9.2 on my ubuntu system (having used Redhat at Uni) and am having real difficulty in getting started, I've tried to find the modeller.top file and also tried to find a comprehensive instructions to help me setup but a lot of it is too advanced for me? can somebody please point me in the right direction; I'm certain once the modeller.top is up and running I should be able to get it working from then on. Many thanks in advance regards Dan

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Modelling complexes
by saccenti＠cerm.unifi.it 06 Sep '07

06 Sep '07

Hi All, I want to model a complex A1+B1 on a template complex A+B where A and B are proteins. I have only one template available. Does somebody as a warking script to do this? Many thanks Edo -- Dr Edoardo Saccenti CERM Magnetic Resonance Center University of Florence Fiorgen Foundation Via Luigi Sacconi n° 6 50019 Sesto Fiorentino (FI) Italy Tel: +39 055 4574281

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setting distance restraints
by Mike White 05 Sep '07

05 Sep '07

I am trying to incorporate some experimentally-derived distance restraints into a homopentamer model, and had a few questions: 1.) the manual says that restraints.make_distance() should be used for setting physical distance restraints. However,in the section on restraints.add() http://salilab.org/modeller/manual/node209.html, an example is given on setting distance restraints with this instead of restraints.make_distance(). Is there any benefit to using one versus the other? Do you use the rsr.add() if you have a lot of restraints to add (as I do- 15 in all)? 2.) restraints.make_distance() uses an analytic model to calculate standard deviations, and the manual says to use model 5 for Calpha-Calpha distances and model 6 for N-O distances. I have not been able to find a description of these models, or which one to use for other atom-pair distances. Does it really make much difference? I did try a quick modeling using restraints.add with the following line in the script: rsr.add(forms.gaussian(group=physical.xy_distance,feature=features.distance(at['ND2:93'],at['NH1:905']),mean=19.3,stdev=0.2)) and got the following error message: ************************************************************************** File "EnforceSymmetryTrim_distance_restraints.py", line 96, in ? a.make() File "/usr/lib/modeller9v2/modlib/modeller/automodel/automodel.py", line 99, in make self.homcsr(exit_stage) File "/usr/lib/modeller9v2/modlib/modeller/automodel/automodel.py", line 423, in homcsr self.mkhomcsr(selection(self), aln) File "/usr/lib/modeller9v2/modlib/modeller/automodel/automodel.py", line 506, in mkhomcsr self.special_restraints(aln) File "EnforceSymmetryTrim_distance_restraints.py", line 37, in special_restraints feature=features.distance(at['ND2:93'], at['NH1:905']), File "/usr/lib/modeller9v2/modlib/modeller/coordinates.py", line 137, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9v2/modlib/modeller/util/modutil.py", line 19, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9v2/modlib/modeller/coordinates.py", line 47, in _indxatm raise KeyError, ("No such atom: %s" % indx) KeyError: 'No such atom: ND2:93' ************************************************************************* which suggests that it can't find the ND2 atom in residue 93 . However, the atom does exist in the *.ini file (as does atom NH1 in residue 905): ATOM 783 ND2 ASN A 93 30.499 39.522 -12.905 ATOM 7622 NH1 ARG E 905 45.372 32.420 -16.993 any ideas as to what is going on here? Thanks Mike White

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structural docking
by rgerber2＠bigred.unl.edu 04 Sep '07

04 Sep '07

Hi I was wondering if it was possible, given two protein sequences or structures, to show possible docking interactions between the two proteins? And if so, how this is done?? Thanks for your time, Ryan

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Loop refinement
by ESTER FUSTE DOMINGUEZ 30 Aug '07

30 Aug '07

Dear Sir/madam, I built a model of a protein using Modeller, and with the PDB file obtained, I'm trying to model loops. I follow the online manual instructions "refining an existing PDB file". However, when I run mod9v2 I obtain this error:( "No such residue: %s" % indx ) Key Error: no such residue 266. In the logfile I don't see what is wrong, and in PDB file 266 residue exists, this is why I don't understand the error "no such residue 266". And could I model three loops at the same time? Thanks. Ester ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

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platform (in)dependent libraries?
by Mike White 28 Aug '07

28 Aug '07

Hi there, I am running Modeller 9v2 on a 64-bit Linux (Suse) box, and when I ran a small test program, it ran fine (as evidenced from the results and log file), but I received the following errors: ******************************************************************** mike@linux-8h71:~/Modelling_projects/Test_Mod9v2> mod9v2 MakePAPFile.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback ******************************************************************* This may have something to do with the directories that various things are in. mod9v2 lives in usr/bin/ the actual programs reside in usr/lib/modeller9v2/ and Python (2.3, 2.4, and 2.5) live in usr/lib64/ Two questions: (1) Is this error something to worry about? (2) If so, how do I correct this problem? As you can guess from the questions, I'm still feeling my way around Linux Thanks Mike White

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multiple-template no overlap
by jinlian05＠lzu.cn 28 Aug '07

28 Aug '07

Hi: My target protein is a member of GPCR.I used multiple template to build the model, there was no overlap among the templates. The final model was not reasonable. The C-tail and N-tail were away from transmember region, simultaneity,located flank of transmember region.I want to know, was there any restraints on 'MODELLER'? the following is alignment: >P1;proteinA structureX:proteinA aaaaaaaaaaaaaaaaaaaaaaaaaaaa----------------------------------* >P1;proteinB structureX:proteinB ----------------------------bbbbbbbbbbbbbbbbbbbbbbbbb---------* >P1;proteinC structureX:proteinC -----------------------------------------------------ccccccccc* >P1;model sequence:model aaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbcccccccccc* The following was my script: from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='model_mult.ali', knowns=('proteinA','proteinB', 'proteinC' ), sequence='model') a.starting_model = 1 a.ending_model = 1 a.make() was I missing something important? Or, did it in a wrong way? looking for your reply! thanks!

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Problem when reconstruct the protein with know structure!
by liu xin 28 Aug '07

28 Aug '07

Hi all I divided the protein with know structure (bovine rhodopsin receptor) into three part: N-terminus region, transmembrane region and C-terminus region without change their initial coordinates, and I try to use the three parts to reconstruct the original structure of the protein. First, I aligned the three parts as the following way: (sorry, last letter I submited a wrong alignment,the following is I used) >P1;N-terminus structureX:N-terminus aaaaaaaaaa------------------------------* >P1;tm-region structureX:tm-region ----------bbbbbbbbbbbbbbbbbbbb----------* >P1;C-terminus structureX:C-terminus ------------------------------cccccccccc* >P1;original sequence:original aaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb* then I used the following script to generate the original structure of my protein: from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='bhro_mult.ali', knowns=('bhro_n','bhro_tm','bhro_c'), sequence='bhro') a.starting_model = 1 a.ending_model =1 a.make() However, the generated model was different from the original one, looking closely, I found the difference mainly occurred in the N-terminus and C-terminus regions, their coordinates have changed greatly when compared with the original structure. I was missing something important? Or, did it in a wrong way? I am new to modeller, any suggestions are appreciated! Thanks in advance yours Xin Liu

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