Dear Pawel,
Could you try the web-based version of MODELLER to accomplish this task and see if this suits your needs:
1) Go to http://structuropedia.org 2) Under the TRANSFORM menu, choose "Superposition" and follow the instructions by clicking on the "i" icon.
With warmest regards,
*AMJAD FAROOQ PhD DIC | Associate Professor*Dept of Biochemistry, University of Miami School of Medicine *Location*: Gautier Building, Suite 217 *Address*: 1011 NW 15th Street #217, Miami , FL 33136, USA *Contact*: amjad@farooqlab.net | 305-243-2429 *Labpage*: farooqlab.net | structuropedia.org
On Mon, Jun 15, 2015 at 6:18 AM, Pawel Kedzierski < pawel.kedzierski@pwr.edu.pl> wrote:
> Dear modellers, > possibly I have posted too long message so no one got through to my > questions. > Let me take it to the basics, then: > > How to reliably calculate the minimum RMSD (and superposition) between CA > carbons, based on sequence alignment? > > This simply does not work for me. > Steps to reproduce the problem using modeller examples are described in > the message cited below. > Thanks in advance, > Paweł Kędzierski > > W dniu 06.06.2015 o 10:49, Pawel Kedzierski pisze: > > Dear Modeller users, > > I beg your kind help or explanations for I feel quite at loss with > calculation of structure-structure alignments and optimal RMSD > superpositions with modeller. > > At first, I found it quite problematic to produce homology models > properly superimposed on templates. I started with seemingly simple > idea using automodel class, namely adding: > > a.final_malign3d = True > > to the model-default.py script from modeller examples. The result was > that the final superposition identified just 8 equivalent CA-CA > pairs, for which the RMSD CA was evaluated as 2.79A. > However, when I superimposed the very same pair of structures (model > 1fdx on 5fd1 template) and calculate RMSD CA in another program using > all 54 CA-CA pairs according to alignment.ali used by model-defult.py, > I got 0.5A. > As for the automodel class, intended for simple use, it surprised me > that quite basic task as RMSD CA superposition is not done correctly. > By "correct" or at least the most basic way I understand the superposition > giving the minimum of RMSD using all CA atoms equivalent according to the > alignment. > Maybe I used wrong functionality but I have not found an alternative in > the documentation for the automodel class. > > Finding the automated final multiple structure alignment unreliable, > I started looking into proper ways of superimposing structures. I have > read the documentation on alignment.malign3d and finding it obsolete, on > alignment.salign. Now I am at least able to calculate alignments based > on sequence similarity only and use them to superimpose structures. > However, I am still not able to calculate/improve the alignments based > on structure-structure similarity, and again this seems due to > insufficient number of equivalent CA-CA pairs identified by modeller. > > This is the code I tested, using the structures from modeller examples. > First, sequence-sequence alignment (which works): > > from modeller import * > env = environ() > env.io.atom_files_directory = ['.', 'atom_files'] > mdl = model(env) > aln = alignment(env) > for code in '1fas', '2ctx': > mdl.read(file=code) > aln.append_model(mdl, align_codes=code, atom_files=code) > aln.salign(rr_file='${LIB}/blosum62.sim.mat', > feature_weights=(1,0,0,0,0,0), > improve_alignment=True, > similarity_flag=True, # The score matrix is not rescaled > rms_cutoff=300, > current_directory=True, write_fit=True, > fit=True, fit_atoms="CA", > output='ALIGNMENT QUALITY') > aln.write(file='test1.ali') > > The above part produces sensible sequence alignment in test1.ali and it > reports 61 equivalent CA-CA pairs, but structures saved in the files > 1fas_fit.pdb and 2ctx_fit.pdb are NOT superimposed. > I can, however, use the aln object from above to correctly superimpose > structures with model and selection classes: > > mdl.read(file='1fas') > sel = selection(mdl).only_atom_types('CA') > mdl2 = model(env, file='2ctx') > sel.superpose(mdl2, aln) > mdl.write(file='1fas_fit2.pdb') > mdl2.write(file='2ctx_fit2.pdb') > > Now the structures written out to 1fas_fit2.pdb and 2ctx_fit2.pdb ARE > superimposed. They are however different enough that only 5 equivalent > CA-CA pairs within 3.5A cutoff are reported. > I am able to confirm that with sufficiently large cutoff, there are 61 > CA-CA pairs, consistently with the alignment aln (checked by > examination of the test1.ali file). Such confirmation is produced with: > > aln.compare_structures(rms_cutoffs=[999]*11) > > Finally, what does not work for me at all is when I try to improve the > alignment based on structure-structure similarity. The command below - > as a continuation of the previous code snippets - fails with the > exception that the number of equivalent positions is 0: > > aln.salign(fit=True, fit_atoms="CA", > feature_weights=(0,1,0,0,0,0), > rms_cutoff=1000.0, > improve_alignment=True, > current_directory=True, write_fit=True, > output='ALIGNMENT QUALITY') > > Questions: > 1. Why it fails, if the previous checks find at least 5 equivalent > positions even with the default cutoff (3.5), and with the > rms_cutoff=1000.0 and fit_atoms="CA" there should be 61 equivalent > positions according to the alignment? > > 2. Why the first salign invocation has saved structures which were not > superimposed, incoherently with the options fit=True, write_fit=True? > > 3. How one shoud use the salign function to reliably calculate optimal > structure-structure alignment, or optimize some initial one as I tried > to do? > > Thanks in advance, > Paweł Kędzierski > > > > > > _______________________________________________ > modeller_usage mailing listmodeller_usage@salilab.orghttps://salilab.org/mailman/listinfo/modeller_usage > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >