Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 62

-- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Tue, 5 Apr 2011 10:43:50 +0530 (IST) From: Ashish Runthala ashishr@bits-pilani.ac.in Subject: Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 61 To: modeller usage modeller_usage@salilab.org Message-ID: 21943615.630261301980430322.JavaMail.root@mailserver.bits-pilani.ac.in Content-Type: text/plain; charset=utf-8 Sir, *****The whole protein will be moved, of course, but only the RMSD of the selection will be minimized.********** This is not the case. When we use the rotation and translation matrices, on X,Y, and Z sequentially as i did in my program, even if you specify chunk length, entire matrix is translated, you don't choose a subset there. So entire matrix transformation takes place. But lastly for RMSD fit, you just check for selected atoms. Hence, RMSD displayed seems for chunk, but in background entire protein RMSD can be computed, which is not asked by the user. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" modeller_usage-request@salilab.org To: "modeller usage" modeller_usage@salilab.org Sent: Tuesday, April 5, 2011 5:36:59 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 61 Send modeller_usage mailing list submissions to modeller_usage@salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request@salilab.org You can reach the person managing the list at modeller_usage-owner@salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: salign: specify chains to superpose (Modeller Caretaker) 2. Modeller 9.9 release (Modeller Caretaker) 3. modelling a protein withtow chains (Houcemeddine Othman) ---------------------------------------------------------------------- Message: 1 Date: Fri, 01 Apr 2011 13:47:28 -0700 From: Modeller Caretaker modeller-care@salilab.org Subject: Re: [modeller_usage] salign: specify chains to superpose To: Yingjie Lin Yingjie.Lin@mssm.edu Cc: modeller modeller_usage@salilab.org Message-ID: 4D9639E0.7020406@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 03/31/2011 09:08 AM, Yingjie Lin wrote: > I wonder what is the best way to superpose two multi-chain proteins, > and explicitly specify the chains to include in superposition. I know > that I can read only the wanted chains into the alignment, but I also > want to make sure that the other chains move according to the > superposition. Just to be clear here, we should distinguish structural *alignment* (which is what SALIGN does) from superposition (which is what selection.superpose() does). Superposition simply rotates and translates one protein, without changing the alignment, to minimize the RMSD between Calpha atoms in aligned residues. Structural alignment also adds or removes gaps, changing the aligned residues. If you really want to do superposition, simply use selection.superpose() and just give it a selection of atoms in the chains you want to superpose. The whole protein will be moved, of course, but only the RMSD of the selection will be minimized. If you want to do a structural alignment, your first suggestion is probably better - read in just the chains you want, make the alignment, then rotate and translate the full protein accordingly. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Mon, 04 Apr 2011 12:03:57 -0700 From: Modeller Caretaker modeller-care@salilab.org Subject: [modeller_usage] Modeller 9.9 release To: modeller_announce@salilab.org, modeller_usage@salilab.org Message-ID: 4D9A161D.50202@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed The new version of Modeller, 9.9, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.9 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.9 is primarily a bugfix release relative to the last public release (9v8). Major user-visible changes include: # The Windows version of Modeller is now only supported on XP Service Pack 2 or later. If you want to run Modeller on Windows 98, ME, 2000, or NT, use Modeller 9v8. # Added support for Python 2.7 to Windows and Linux Modeller; Python 2.5 is now supported on all platforms. # Initial models generated by automodel now always contain valid PDB coordinates, i.e. each coordinate is in the range -999.999 to 9999.999. # During loop modeling, if atoms are missing from the initial model, loopmodel.loop.write_defined_only can be set True to write out PDBs containing only non-loop atoms present in the initial model. # When reading new-style PDB files (with element names in columns 77-78) Modeller will now use this information to determine whether an atom is a hydrogen. (With old-style or non-conformant PDB files, it will continue to guess based on the atom name, so will not read mercury ions for example unless env.io.hydrogen=True, since it cannot unambiguously determine whether HG is mercury or "hydrogen bonded to CG".) See the Modeller manual for a full change log: http://salilab.org/modeller/9.9/manual/node38.html If you encounter bugs in Modeller 9.9, please see http://salilab.org/modeller/9.9/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 3 Date: Tue, 5 Apr 2011 01:06:57 +0100 From: Houcemeddine Othman houcemoo@gmail.com Subject: [modeller_usage] modelling a protein withtow chains To: modeller_usage@salilab.org Message-ID: BANLkTikUh9qOU-NsGxRqOB4+Q7Dqy+uTWg@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1" Hi I try to model an heterodimer using this alignment >P1;1DZB2 structureX:1DZB2:1:A:107:B:::: QVKLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCAR-----WDWYFDVWGQGTTVTVSSG/ ------------DIELTQSPSSMYTSLGERVTITCKASQDINSYLRWFQQKPGKSPKTLIYYATSLADGVPSRFSGSGSGQDYSLTISSLESDDTTTYYCLQHGESPYTFGGGTKLEIK---------* >P1;atc sequence::::::::: -VKLQQSGGGLVQPGGSLKLSCAASGFDFSRYWMSWVRQAPGKGLEWIGEINPDSSTINYTPSLKDTFIISRDNAKNTLYLQMSKVRSEDTALYYCARQGYDGYHWYFDVWGQGTTVTVSSE/ SLDLGGGGGGGGDIQLTQSPSSLSASVGETVTLTCGASENIYGGLNWYQRKQGKSPQLLIYGATKLADGMSSRFSGGGSGRQYFLKITSLHPDDVATYYCQNVLSNPLTFGAGTKLELKRADAAPTVS* each time it gives me this error message define__595E> Number of selected atoms in sets 2 & 3 is not the same: 121 128 Can you tell me please what's wrong in my alignment file script used: # Homology modeling by the automodel class # # Demonstrates how to build multi-chain models, and symmetry restraints # from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) env = environ() # directories for input atom files env.io.atom_files_directory = './' a = MyModel(env, alnfile = 'ali.pir', knowns = '1DZB2', sequence = 'atc') a.starting_model= 1 a.ending_model = 1 a.make()