April 2011 - modeller_usage

Modeller 9.9 release
by Modeller Caretaker 04 Apr '11

04 Apr '11

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(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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salign: specify chains to superpose
by Yingjie Lin 01 Apr '11

01 Apr '11

Hi Modellers, 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. Here are two ways we could think of: 1. read only the wanted chains and do superposition. Then move the other chains accordingly using functions like selection.rotate_origin(), selection.rotate_mass_center() and selection.transform(). 2. model1 <= all chains in protein A model2 <= all chains in protein B model3 <= the chain(s) selected for superposition in protein B first, superpose model3 to model1 (model3 is moved) second, superpose model2 to model3 (model2 is moved) Are there any better ways? Thank you. Yingjie

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Are gap in target and template same.
by Ashish Runthala 01 Apr '11

01 Apr '11

Dear Modellers, I am facing an interesting problem. Are gaps in target and template same, as shown below. Target AAAAA AA--A AA--A Template AA--A AAAAA AA--A CaseI CaseII CaseIII Are these three cases I,II, & III modelled the same way. How will the gap penalties be incorporated in these three cases, when the modeller calculates the alignment score. PLEASE PROVIDE ME COMPLETE DETAILS ABOUT GAP PENALTIES IN THESE THREE CASES. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 59
by Ashish Runthala 01 Apr '11

01 Apr '11

Dear Lin, I wrote a script in C to do all that. You can use it to do the analysis for specific chains. You can even do the analysis for specific segment of residues in a specific chain. If you want, I will provide you the help by providing the binary. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Friday, April 1, 2011 10:01:26 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 59 Send modeller_usage mailing list submissions to modeller_usage(a)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(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)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. unsubscribing (Bo Yang) 2. salign: specify chains to superpose (Yingjie Lin) 3. salign: specify chains to superpose (Yingjie Lin) 4. Are gap in target and template same. (Ashish Runthala) ---------------------------------------------------------------------- Message: 1 Date: Thu, 31 Mar 2011 08:07:11 -0700 (PDT) From: Bo Yang <n62star(a)yahoo.com> Subject: [modeller_usage] unsubscribing To: modeller_usage(a)salilab.org Message-ID: <676504.10553.qm(a)web36906.mail.mud.yahoo.com> Content-Type: text/plain; charset="us-ascii" unsubscribing

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