February 2012 - modeller_usage

Regarding Scoring Parameters
by Ashish Runthala 08 Feb '12

08 Feb '12

Dear Modellers, For E-value and alignment scoring systems, we use the parameters lambda and K. Specifying these scores is must for a scoring system. So what is/are the normal set of these parameters used in PSI-BLAST/CS-BLAST/HHPRED or other profile inclusion based template searching methods? Tell me the commonly used values for these two parameters lambda and K for the calculation of alignment scores. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Regarding Model Clustering
by Ashish Runthala 02 Feb '12

02 Feb '12

Dear Modellers, What is the best way to cluster the high scoring model decoys into a well refined conformation with almost correct domain topology, as existing in the considered models. I tried using transfer_xyz to pool 2 best complete models(being best for each of the 2 individual domains, considered on TM-score,GDT). I also tried building the new model through these 2 models using them as templates in different salign modules, but i failed to improve the model for both the individual domains and the overall model together. For 1 domain my prediction with a set of templates and my representative alignment had GDT-TS of 96.875 for Domain1. For D2 best model, it was 99.645. The moment i used Salign, topology got messed up. So when i just pooled (copied) the individual correct domain coordinates from best models for D1 and D2 into the complete model, RMSD became 2.433 with GDT-TS of just 63.309. WHY IT HAPPENED? So only refinement is used by many CASP9 teams to further refine this topology. But this big difference of GDT-TS can't be corrected by refinement. WHY 2 CORRECT DOMAIN MODELS PUT OR COPIED TOGETHER CAN'T GIVE AN OVERALL CORRECT MODEL. HOW TO USE SPICKER. TELL ME THE CORRECT PATH TO CLUSTER THE MODELS FOR BUILDING AN OVERALL CORRECT MODEL TOPOLOGY. Thanks for support, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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generating homology models of reduced disulfide bonds
by Stephanie Schaefer 02 Feb '12

02 Feb '12

Hello, I recently obtained the xray structure of my wildtype protein which I am using as my template. This protein has a redox active disulfide (an other structural disulfides). I would like to generate homology models in which the redox active disulfide bond is broken (the model would represent the cysteines in a reduced environment). I am new to modeler, but what I have done is edited the template PDB (wildtype) to remove the active site disulfide (SSbond) and then generated a homology model using the modified wt PDB as the template. Is this the correct approach to generating a reduced active site model? If this is not an acceptable approach what would you suggest? Thank you for your time, Stephanie Schaefer University of Delaware Biochemistry PhD Student 302-831-2658

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problems with filling missing residue without moving exing ones
by Francesco Pietra 02 Feb '12

02 Feb '12

I could nicely fill missing residues 519-522 and 683-684 by using the normal protocol at /wiki/Missing residue. However, as I would like the existing residues not being modified, I used a script: from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('518', '521'), self.residue_range('681', '683')) a = MyModel(env, alnfile = 'alignment.ali', knowns = myPDB, sequence = 'myPDB_fill') a.starting_model= 1 a.ending_model = 1 a.make() based on the last part of the wiki. Consistently, the error is: ................................. File "fill_resid_no-move.py", line 20, in ? a.make() File "/usr/lib/modeller9.10/modlib/modeller/automodel/automodel.py", line 106, in make atmsel = self._check_select_atoms() File "/usr/lib/modeller9.10/modlib/modeller/automodel/automodel.py", line 490, in _check_select_atoms atmsel = self.select_atoms() File "fill_resid_no-move.py", line 12, in select_atoms return selection(self.residue_range('518', '521'), File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 304, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 234, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9.10/modlib/modeller/util/modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 298, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 518' I tried different selections as '518', '521' always getting error in finding the first residue in this '...' list. alignment.ali is constructed, as in the wiki, of first the structure, then the sequence. At any event, the alignment.ali is the same that works well with the script that allows all atoms to move. I serched the web; hope this is no duplication. Thanks for advice francesco pietra

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