February 2021 - modeller_usage

Quick Question on Automodel
by Pedro Guillem 08 Mar '21

08 Mar '21

Hello all, I'm trying to model from a known template (ident 37%). The template is missing the first 3 residues in the structure. - I start reading the template at position 4. - I add 3 dashes to the beginning of the template to compensate for the missing residues. (otherwise I get a "residue mismatch" error from modeller) Now, my alignment needs 3 additional gaps at the start of the template. No matter what I do, adding 6 dashes to the beginning of the template (3 for the missing residues and 3 extra for my alignment) has no effect on the outcome and the model doesn't align with the template in the way I expect. Here is a bit of my ali file. I want the TRL of the template to align with the TRM of the sequence. When it finishes, the position of TRM has a different offset in relation to TRL Am i doing something wrong here? >P1;template structureX:template:4:A:330:A:xxxxx:xxxxxxx:2.30:0.211 ------TR*L*......................rest of seq* >P1;seq sequence:seq:.:.:.:.:::: EAARRRTR*M*........ rest of seq* Thanks in advance. Pedro

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remodelling a fragment of protein using different template.
by Yogesh Sharma 16 Feb '21

16 Feb '21

greetings readers, I am trying to model a protein with low homology. I have used ab initio methods to get a starting structure. but i want to remodel first 50-100 residues according to a different PDB template. is it possible to do so using modeller? please give some suggestions *Yogesh Sharma*

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Installation Bug issue modeller 10.0
by Henry Monteiro 07 Feb '21

07 Feb '21

Greetings, I got the keys recently but I stumbled on a problem trying to run the program. When I type and run the command "mod10.0 foo.py" (ubuntu 20.04) this come in response: "Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback FATAL ERROR: Cannot open file foo.py: No such file or directory" Could you guys have any clue how to repair this problem? Sincerely, Henry Magalhães

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Modeller 10.0 release
by Modeller Caretaker 02 Feb '21

02 Feb '21

A new version of Modeller, 10.0, is now available for download! Please see the download page at https://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 10.0 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.0 is a major update that adds support for residue numbers >= 10000 in PDB format files using hybrid-36 notation, assigns the chain ID 'A' to single-chain models to generate more standard PDB files, and uses CamelCase naming for all Python classes. See the Modeller manual for a full change log: https://salilab.org/modeller/10.0/manual/node40.html If you encounter bugs in Modeller 10.0, please see https://salilab.org/modeller/10.0/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 unsubscribe from the modeller_announce mailing list, or reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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