- modeller_usage - salilab.org

Re: [modeller_usage] problem of strand/sheet
by Thomas Evangelidis 01 Sep '10

01 Sep '10

In my case although most of the hydrogen bonds imposed by secondary_structure.sheet() have been satisfied, the 3 strands do not adapt a beta sheet conformation. I tried to optimize only the 3 antiparallel beta strands by adapting the examples/automodel/model-segment.py script. After setting physical.values(default=1.0, h_bond=10.0)I get these violations in my log file: # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 8 H-bonding potential : 20 0 5 0.103 0.103 31.778 10.000 What type of restraints does secondary_structure.strand() impose to scale them up? The manual says phi and psi binormal restraints only, but in my log file I get this: 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 I also need some help interpreting the restraint files: 1. What do the different columns (apparently not the first 2) represent in the target.V99990001 file? 2. For what pattern should I search in the target.rsr file with respect to the beta sheet? Surprisingly I cant find any column having a Group value 8 (the 4th column) which corresponds to the H-bonding potential imposed by secondary_structure.sheet().

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R: modelling discarding part of a template
by Thomas Evangelidis 01 Sep '10

01 Sep '10

> You have to either keep the complete template sequence in the PDB file, > or modify the template PDB to remove the residues you don't want. An > alignment that achieves what you want without modifying the PDB is: > > target: AAAAAAAAAAA-------AAAAAA > template 1: BBBB-------BBBBBBBBBBBBB > template 2: ZZZZZZZZZZZ-------ZZZZZZ > > Ben Webb, Modeller Caretaker > > Is it algorithmically difficult to add a function that will select a range of residue in one template and Modeller will exclude them without touching the alignment? When having multiple templates and several unwanted regions this procedure becomes very tedious.

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unable to read structural information
by meier＠lmb.uni-muenchen.de 31 Aug '10

31 Aug '10

Hi all, suppose I have the following simple "dummy" py-modeller script: from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = '<path to pdb>' # containing d1f0la3.pdb a = automodel(env, alnfile = '<my_pir_file.pir>', # alignment filename knowns = 'd1f0la3', # codes of the templates sequence ='d1f0la3') # code of the target a.starting_model = 1 a.ending_model = 3 a.make() and the corresponding pir file: >P1;d1f0la3 sequence:d1f0la3: 1: : 180: :f.1.2.1 (A;201-380) Diphtheria toxin, middle domain {Corynebacterium diphtheriae [TaxId; 1717]} PDB; d1ddta3 d1p3gb_ d1p3gf_ d1p3pb_ d1p3pf_ d1p3bf_ d1p3ib_: : 0.00: 0.00 CINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKT TAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAY* >P1;d1f0la3 structureX:d1f0la3: :A: :A:f.1.2.1 (A201-380) Diphtheria toxin, middle domain {Corynebacterium diphtheriae [TaxId 1717]} PDB d1ddta3 d1p3gb_ d1p3gf_ d1p3pb_ d1p3pf_ d1p3bf_ d1p3ib_:Corynebacterium diphtheriae [TaxId; 1717]:-1.00:-1.00 CINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKT TAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGEL--IGFAAYNFVESIINLFQVVHNSYNRPAY* Then I get the following error when executing the script: Traceback (most recent call last): File "/cluster/tmp/armin/test/d1f0la3_d1f0la3_1.py", line 14, in <module> a.make() File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/automodel/automodel.py", line 425, in homcsr self.check_alignment(aln) File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/automodel/automodel.py", line 407, in check_alignment aln.check() File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/alignment.py", line 191, in check self.check_structure_structure(io=io) File "/cluster/bioprogs/modeller9v5_RSR/modlib/modeller/alignment.py", line 200, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.ModellerError: check_a_282E> Unable to read structural information for alignment sequence: 1 d1f0la3 This command requires structures. Any ideas whats wrong? Thanks in advance Armin

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modeller usage under Cyg Win
by Andrew Voronkov 26 Aug '10

26 Aug '10

What version of Modeller is better to use under Cyg win on 64 bit Windows system? I have problems while using the Windows version of the program. Sincerely yours, Andrew

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modeling mutant proteins
by Peter K 26 Aug '10

26 Aug '10

Hi, i would like to know the tool which uses modeller for prediction of structure of mutants and analyze its stability and change in activity in mutant proteins.Can any one suggest a tool for it.

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initial model
by sdh 17 Aug '10

17 Aug '10

Hello All, I want to model a multi-domain protein. Thus, I aligned manually all templates (corresponding to the individual domains) and used them as an input for Modeller. (Note that the templates overlap only over few residues.) However, when I compared the initial model (.ini) to the aligned templates, I saw that Modeller did something more than just transferring the coordinates from the templates. Namely, the relative orientation of domains is not as in my structural alignment. Is thee any way to force Modeller to use exactly the input coordinates? initial_malign3d is set to False and default transfer_xyz() is used Thanks for help! Staszek

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very_fast()
by sdh 17 Aug '10

17 Aug '10

Hello, Does usage of "very_fast()" deactivates restraints defined by "nonstd_restraints()"? sdh

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Parallel task using sge_pe_job()
by Charles Xue 28 Jul '10

28 Jul '10

Hello, I am attempting to run MODELLER in parallel on a cluster with multiple nodes. The script I used is below: from modeller import * from modeller.parallel import * from modeller.automodel import * log.verbose() j = sge_pe_job() env = environ() a = automodel(env, alnfile='2NT2-mult.ali', knowns=('1m3gA','2wgpA','2hxpA'), sequence='2NT2', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 25 a.use_parallel_job(j) a.make() However, once I submit the job (using the parallel environment mpich), the job runs on the master node fine but fails on all the slave nodes. The error is also ambiguous: within the slave1 output file (identical for all other output files except the slave0 one which runs fine): error: executing task of job 76003 failed: Thanks in advance for the help! -Charles Xue

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Re: [modeller_usage] have you solved the problem with installation under Windows XP
by Modeller Caretaker 23 Jul '10

23 Jul '10

On 7/23/10 1:59 PM, Andrew Voronkov wrote: > Here is modenv.bat from 64 bit system. I got no item in Start menu. Your batch file is fine - it's the same as mine. The Modeller shortcut in the Start menu simply runs command.com /E:8192 /K "C:\Program Files\Modeller9v8\bin\modenv.bat" i.e. it starts a command prompt and runs that batch file to set up the environment so that Modeller will work. (If you run a regular command prompt, it won't have the paths set up properly, and Modeller won't work.) I don't know why the Start menu shortcut isn't being installed on your system - although you have to run the installer as an admin user in order for it to do that (it should warn you if you don't) - but you can make your own shortcut to Modeller in this case. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Re: [modeller_usage] have you solved the problem with installation under Windows XP
by Modeller Caretaker 23 Jul '10

23 Jul '10

On 7/23/10 12:48 PM, Andrew Voronkov wrote: > Actually indeed only one PC where I don't have this problem is 32 bit > NoteBook, btw I also have some troubles with rpm usage for 64-bit. What sort of troubles? I can't help you if I don't know what your problem is. > So what can be a soluation for 64 bit system? How batch file is > called? I can't find anything with *batch* in the search. The Modeller batch file is called modenv.bat and lives in the 'bin' directory under whichever directory you installed Modeller in (C:\Program Files\Modeller9v8 by default). On a successful install, it looks like: @echo off set MODINSTALL9v8=C:\Program Files\Modeller9v8 set PYTHONPATH=C:\Program Files\Modeller9v8\modlib; set LIB_ASGL=C:\Program Files\Modeller9v8\asgl set BIN_ASGL=C:\Program Files\Modeller9v8\bin set PATH=%MODINSTALL9v8%\bin;%PATH% cd C:\Program Files\Modeller9v8 echo You can find many useful example scripts in the echo examples\automodel directory. echo Type 'mod9v8' to run Modeller. What does yours look like? Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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