July 2010 - modeller_usage

questions about model refinement protocol
by albert 06 Jul '10

06 Jul '10

Hello: I am reading Modeller9v8 manual and found in Page 14, 2.2.2, it is said that models could be refined by VTFM with conjugated gradients(CG) methods. In fact CG is usually applied to correct subtle errors and steepest gradient (SG) is effective for some big erros. I am wondering why not import SG for model refinement? In fact, I found that may people would like to do SG before CG when they are doing model refinement. Thank you very much.

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job running error
by albert 06 Jul '10

06 Jul '10

Hello: I am running modeller job by "python model-parall.py" based on the following scrips. But it is said in the termial which seems that modeller coundn't find the template pdb file. However, my template pdb file is already in the same working directory which named pt6A.pdb. I don't why it said couldn't find it. Would you please give me some advices? File "/soft/python2.5/lib/python2.5/site-packages/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/soft/python2.5/lib/python2.5/site-packages/modeller/automodel/automodel.py", line 411, in homcsr aln = self.read_alignment() File "/soft/python2.5/lib/python2.5/site-packages/modeller/automodel/automodel.py", line 401, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/soft/python2.5/lib/python2.5/site-packages/modeller/alignment.py", line 81, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = pt6 ---------------------------------------------------------------------------------------- # Homology modeling by the automodel class, using multiple processors from modeller import * from modeller.automodel import * # Load the automodel class from modeller.parallel import * # Use 2 CPUs in a parallel job on this machine j = job() j.append(local_slave()) j.append(local_slave()) log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env, alnfile = 'a8-pt6.ali', # alignment filename knowns = 'pt6', # codes of the templates sequence = 'a8') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.use_parallel_job(j) # Use the job for model building a.make() # do the actual homology modeling

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Re: [modeller_usage] questions about loop refinement
by David Hall 05 Jul '10

05 Jul '10

http://www.salilab.org/modeller/manual/node90.html ? -David On Jul 4, 2010, at 10:25 AM, albert <leuven(a)yeah.net> wrote: Hello I have see the ppt in Modeller website and it is said that in Modeller9V8 has a new method for loop building and refinement, i.e: Newer DOPE + GB/SA protocol("dope_loopmodel"). However, in the lastest Modeller manual I don't find such kind of function. I would be very appreciated if someone could tell me how to use this new function or where I can find a scrips of Modeller. Thank you _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage

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questions about loop refinement
by albert 04 Jul '10

04 Jul '10

Hello I have see the ppt in Modeller website and it is said that in Modeller9V8 has a new method for loop building and refinement, i.e: Newer DOPE + GB/SA protocol("dope_loopmodel"). However, in the lastest Modeller manual I don't find such kind of function. I would be very appreciated if someone could tell me how to use this new function or where I can find a scrips of Modeller. Thank you

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questions on loopmodel in the presence of a ligand
by Diane Lynch DLLYNCH 02 Jul '10

02 Jul '10

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Cross Species Dimer
by Fuhrman, Kit 02 Jul '10

02 Jul '10

Dear Modellers, I am looking for some insight into modeling a heterodimeric complex in a single species. The original crystal structure was solved with Chain A and Chain B from two different species. Chain A is from humans and Chain B is from mice. I would like to model the whole complex in the mouse form. Chain A is about 77% conserved between mice and humans. Here's my basic protocol. 1) I edited my sequences to contain only the portions modeled in the PDB. 2) I used align2d to create my PIR and PAP files 3) I used automodel and subclassed it to only select chain A for modeling The final structure looks ok visually. The DOPE score per residue actually decreased by about .01 for a few regions between the crystallographically solved structure and final homology model. Otherwise is looks about the same. Does this protocol sound correct? Is there anything else I should have done? or other potential problems I should look out for? My main concern is that the dimer interface be as close to the real deal as possible. I ran one of the models through PDBsum and a couple of Gamma turns were lost. One turn had the same sequence in both human and mouse, but no did not show up as having the secondary structure. Any help would be greatly appreciated. Best regards, Kit Kit Fuhrman IDP Graduate Student Department of Pathology, Immunology and Laboratory Medicine University of Florida College of Medicine kit.fuhrman(a)pathology.ufl.edu

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