- modeller_usage - salilab.org

Modeller 9v7 release
by Modeller Caretaker 16 Jun '09

16 Jun '09

The new version of Modeller, 9v7, 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 9v7 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9v7 is primarily a bugfix release relative to the last public release (9v6). Major user-visible changes include: # A new method alignment.get_suboptimals() allows the suboptimal alignment file generated by alignment.salign() to be easily parsed. # A new method iterative_structural_align() provides a straightforward way to obtain the best SALIGN structure-structure alignment. # alignment.append() and alignment.read_one() now take a new argument, allow_alternates, which allow for alternate matches of one-letter codes when reading PIR sequence ranges from PDB files (B to N, Z to Q). # Parallel jobs have a new method, job.yield_tasks_unordered(), which is like job.run_all_tasks() but which returns results as they are generated rather than when all the tasks have finished. # Parallel jobs now default to trying to duplicate the current Python environment (using modslave.py and modpy.sh if necessary) when setting modeller_path, rather than running the mod9v7 script, since the latter may conflict with the Python version of the master. See the Modeller manual for a full change log: http://salilab.org/modeller/9v7/manual/node38.html If you encounter bugs in Modeller 9v7, please see http://salilab.org/modeller/9v7/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 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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Modeller output directory
by Riadh HAMMAMI 16 Jun '09

16 Jun '09

Hello, I have a problem concerning the output directory in modeller. I’m running script from different location (“mod9v6 /script/location/model-full.py”). The generated models (including other files) are located in the running folder. I would like to set the output directory to a fixed location (for e.g. the same of the script “/script/location/”). is there any issue ? Thank you for your help, Riadh

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problem with hetrotetrameric protein
by subarna thakur 02 Jun '09

02 Jun '09

Hello I facing a problem for building a model of a hetrotetrameric protein with 4 chain. Chain A and C are similar and have 423 aminoacids while chain B and D have 504 amino acids. The template I am taking is also a hetero tetrameric protein. Can any body please tell me how to write the header of the alignment file of the template as well as my target protein. The example given in the manual isnt quite helpful as it shows the case where there is just two chain. Subarna Thkur Explore your hobbies and interests. Go to http://in.promos.yahoo.com/groups/

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(no subject)
by subarna thakur 29 May '09

29 May '09

Hi I am using the model-ligand.py script. My protein in multi-chained, do I have to make changes in the header of the aligenment file? I have put (.) sign at the end of the alignment file and also made option env.io.hetatm is set to True but when I am running the model-ligand.py, a error is coming that there is a mismatch between the alignment and PDB. Subarna Thakur Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/

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how add FE-S cluster in PDB
by subarna thakur 29 May '09

29 May '09

Dear User My template has a ligand of Fe-S cluster but when I am generating my PDB file based on this template, it is without any metal ligand..I want to know how do I incorporate the metal cluster in correct position in my PDB file. Subarna thakur Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com

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Re: [modeller_usage] loop refining of a multi chain protein
by subarna thakur 29 May '09

29 May '09

Dear Sir Thanks for suggestion ,it worked. After running the script two PDB files are generated one with extension .BL00010001 and other with .IL00000001 extension.Which one should I select and on which basis? ________________________________ From: Dinesh Babu KR <kr.dineshbabu(a)gmail.com> To: subarna thakur <thakur.subarna(a)yahoo.co.in> Sent: Friday, 29 May, 2009 11:51:19 AM Subject: Re: [modeller_usage] loop refining of a multi chain protein hi in the loop script file you have to mention the chain like this self.residue_range('77:B', '80:B') regards, dinesh On Fri, May 29, 2009 at 1:49 PM, subarna thakur <thakur.subarna(a)yahoo.co.in> wrote: Dear User I have a protein with multichain and I am using loop.py script for refining a protein but a error is coming which suggests that it fails to indentify the metioned residues in pdb file. But when I am running the same loop.py script with a alignment file and PDB file without mentioning any chain, it seems to run ok.. In case of multichain proteins what should be the changes made to the loop.py script for loop refining and how the residues should be mentioned in the script. Subarna thakur ________________________________ Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com

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loop refining of a multi chain protein
by subarna thakur 28 May '09

28 May '09

Dear User I have a protein with multichain and I am using loop.py script for refining a protein but a error is coming which suggests that it fails to indentify the metioned residues in pdb file. But when I am running the same loop.py script with a alignment file and PDB file without mentioning any chain, it seems to run ok. In case of multichain proteins what should be the changes made to the loop.py script for loop refining and how the residues should be mentioned in the script. Subarna thakur Share files, take polls, and make new friends - all under one roof. Go to http://in.promos.yahoo.com/groups/

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Fully automated alignment and modeling
by mzugravu＠buffalo.edu 27 May '09

27 May '09

Hello everyone! I'm trying to do fully automated alignment and modeling on a target sequence having a template sequence. Could you please tell me where I can create .py (python) files and .erg files like the ones used in the online tutorial page Fully automated alignment and modeling? Thank you very much.

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(no subject)
by Ha Hung Chuong Nguyen 27 May '09

27 May '09

Hi mzugravu, I guess there are at least some. In my case, when I have the alignment, I often using Jalview to open it and export to PIR format. Bests, Chuong mzugravu(a)buffalo.edu wrote: > Hello! > Could you please tell me which program should I use to write an alignment file in the PIR format? > Thank you. > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/

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alignment file in the PIR format
by mzugravu＠buffalo.edu 27 May '09

27 May '09

Hello! Could you please tell me which program should I use to write an alignment file in the PIR format? Thank you.

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