- modeller_usage - salilab.org

refining bad backbone & side chain angles
by Irene Newhouse 08 Dec '10

08 Dec '10

Following an earlier message on the topic of refining a homology model, I just tried a Chimera minimization. The results underwhelm me: Procheck before minimization had 34/576 residues marked with bad phi, psi angles & 10 with bad chi angles. After minimization, there were 40 residues with bad phi, psi angles & 11 with bad chi angles. That's NOT the direction I was looking for! The template structure contained 454 residues, of which only 2 were marked for phi, psi angles by Procheck, and 4 for chi angles. There's only 27% identity, so that's probably part of the issue. Any recommendations? Thanks! Irene Newhouse

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mutant two ore more residues
by Knut J Bjuland 03 Dec '10

03 Dec '10

I have made some modification to the mutant script at the modeller wiki. The change may be seen as patch to the original file. I I whised to change residue 1M and 3P to 1T and E3 in 1B72 is this the way to go. Ca s.mutant be used to select two residues? Knut J --- mutant.py 2010-12-01 09:04:33.004206998 +0100 +++ mutant2.py 2010-12-01 13:09:02.334207000 +0100 @@ -65,7 +65,7 @@ spline_on_site=True) #first argument -modelname, respos, restyp, chain, = sys.argv[1:] +modelname, respos, restyp, chain, respos2, restyp2, chain2 = sys.argv[1:] log.verbose() @@ -98,6 +98,12 @@ #perform the mutate residue operation s.mutate(residue_type=restyp) + + +s1=selection(mdl1.chains[chain2].residues[respos2]) +s1.mutate(residue_type=restyp2) + + #get two copies of the sequence. A modeller trick to get things set up ali.append_model(mdl1, align_codes=modelname) @@ -145,26 +151,30 @@ #residue, in second pass, include nonbonded neighboring atoms) #set up the mutate residue selection segment s = selection(mdl1.chains[chain].residues[respos]) - +s1=selection(mdl1.chains[chain2].residues[respos2]) mdl1.restraints.unpick_all() mdl1.restraints.pick(s) s.energy() +s1.energy() s.randomize_xyz(deviation=4.0) +s1.randomize_xyz(deviation=4.0) mdl1.env.edat.nonbonded_sel_atoms=2 optimize(s, sched) +optimize(s1, sched) #feels environment (energy computed on pairs that have at least one member #in the selected) mdl1.env.edat.nonbonded_sel_atoms=1 optimize(s, sched) +optimize(s1, sched) s.energy() - +s1.energy() #give a proper name -mdl1.write(file=modelname+restyp+respos+'.pdb') +mdl1.write(file=modelname+restyp+respos+'_'+respos2+restyp2+'.pdb') #delete the temporary file os.remove(modelname+restyp+respos+'.tmp')

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error using mutate_model.py
by Anna Marabotti 01 Dec '10

01 Dec '10

Hi, I tried to apply the script mutate_model.py to introduce a single point mutation on a protein, and I obtained an error: I'm attaching here the .log file. >From the error message, I see that mutate_model seems to be unable to manage a protein with chain breaks. I can obviously follow the suggestion and relabel the chains of my protein; however, chain breaks are a quite common situation in PDB files, therefore I wonder if there is a way to correct this problem without changing the chain ID as suggested in the log file (which is formally uncorrect since I don't have multiple chains in my protein). Any help will be appreciated. Many thanks in advance and best regards Anna Marabotti __________________________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabotti(a)isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a man with a gun meets a man with a pen, the man with the gun is a dead man"

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A better way to do this?
by Stéphane Téletchéa 01 Dec '10

01 Dec '10

Dear users, I'm willing to create a peptide sequence from a fasta sequence, and add a disulfide bridge in it. At the moment, my code "which works" is like this pseudo-code: 1 - create a model object, and model.build('sequence'), I am not applying any time of secondary structure constraint 2 - write this pdb (peptide.pdb) 3 - create a special align where target and template are identical (peptide.ali) 4 - create a new object, Mymodel derived from automodel to add the patch for disulfides 5 - generate models 6 - select the best one (peptide-cys.pdb) I'm only willing to retrieve the "peptide-cys.pdb" file, can I bypass steps 2,3 and act directly on the initial model object created? The implementation of the pseudo-code above is: ##################################################################### # This demonstrates the use of alignment.append_sequence() and # model.build_sequence() to build residue sequences from one-letter codes # http://salilab.org/modeller/manual/node171.html from modeller import * from modeller.automodel import * env.libs.topology.read('${LIB}/top_heav.lib') env.libs.parameters.read('${LIB}/par.lib') # Create a new empty alignment and model: aln = alignment(env) mdl = model(env) mdl.build_sequence('ACAAAAACYAAAA') mdl.write(file='pept.pdb') class MyModel(automodel): def special_patches(self, aln): # The disulfide bridge is taken from the input sequence self.patch(residue_type='DISU', residues=(self.residues['2', self.residues['8'])) a = MyModel(env, alnfile = "tmppiralign.ali", knowns = "pept", sequence = "pept-cys") a.starting_model= 1 a.ending_model = 10 a.make() ##################################################################### tmppiralign.ali is of the form: ##################################################################### >P1;pept structureX:pept:1: :13: :::: ACAAAAACYAAAA* >P1;pept-cys sequence:pept-cys::FIRST:@ END ::::: ACAAAAACYAAAA* ##################################################################### Thanks a lot for corrections, suggestions,.. Stéphane

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C0-0rdinate bond generation
by SR.Sathya Baarathi 29 Nov '10

29 Nov '10

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Modeling ...
by bharat lal 29 Nov '10

29 Nov '10

Hi Everybody, I want to insert a peptide fragment into one of the loops of my template protein structure .. Can anybody tell me how can I do it .. Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 E-mail : monu46010(a)yahoo.com

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measure protein stability
by Knut J Bjuland 29 Nov '10

29 Nov '10

I have designed a homolog protein with sequence identity above 90 %? How can I measure protein stabilty and it ability to form aggreation. An example would be amyloid plage which aggregat in Alzheimer disease? Can I use dope score to measure protein stability or should I turn to rosetta desginer? Knut J

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Heme iron
by flavio seixas 29 Nov '10

29 Nov '10

Hi, I am modellig a structure of an hemoglobin with the four heme groups bonded to oxygen. To do the alignment I refer to heme as "h" and oxygen as "o". The template model is the oxy hemoglobin at 1.25 Angstrons resolution Pdb id: 2DN1. The final model has heme and oxygen, but the iron configuration is OUT of the plane of porphyrin ring toward proxymal His which is bonded to iron. This configuration is different as observed in oxygen ligated form of hemoglobin in which the iron is in the SAME plane of the porphyrin ring. In summary, the final model has an heme group in a configuration observed in deoxy form (iron out of the porphyrin plane). I wish it looks like appears in oxy form (iron inside the porphyrin plane). I appreciate any kind of suggestions. Flavio

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umber of equivalent positions < 3
by bharat lakhani 29 Nov '10

29 Nov '10

Hi Everyone, I am getting this error, when i am running modeller. i posted this mail before but i did not get any reply. looking forward to it Traceback (most recent call last): File "compare_1.py", line 32, in ? aln.malign3d() File "/usr/lib/modeller9v8/modlib/modeller/alignment.py", line 329, in malign3d edit_file_ext) _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 1

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Re: [modeller_usage] high model clashscore
by Nick Burton 22 Nov '10

22 Nov '10

Hello, I have found that, in many cases, switching on the Lennard-Jones restraint (energy_data.dynamic_lennard = True) and up-weighting it with respect to other restraints (env.schedule_scale...) can reduce the bad van der Waal's interactions as measured by Molprobity. Cheers, Nick On 20 November 2010 13:03, Anton Iershov <" target="_blank">a.yershov(a)yahoo.com> wrote: Dear Modeller Caretaker, When performing homology modeling with default parameters ("model-default.py") and subsequent analysis with Molprobity (http://molprobity.biochem.duke.edu/) I obtain models with much more high clashscore than the template has, and model optimization does not help much. Then, Kinemage (http://kinemage.biochem.duke.edu) shows a lot of "bad" van der Waals contacts. What should I do to obtain model of higher quality (I mean to reduce clashscore and number of "bad" contacts)? Thanks in advance, Anton. ---------------------- Dr N M Burton Department of Biochemistry University of Bristol BS8 1TD, UK +44 117 3312149 nick.burton(a)bristol.ac.uk

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