March 2021 - modeller_usage

Adding glycans in AutoModel?
by Steven Truong 19 Mar '21

19 Mar '21

Dear Modeller Mailing List, I was hoping to ask if there is a way to automate glycan-building in Modeller. I’ve been able to get all residues/atoms built using AutoModel. However, I lose the glycan information when using AutoModel. Is there another program that interfaces well with Modeller, or is there a class in Modeller that can add glycans at known positions (e.g. if I know NAG is attached to residue 6, can I add that to the PDB output somehow?). Thank you! Steven Truong sdt45(a)cam.ac.uk<mailto:sdt45@cam.ac.uk> Cambridge University

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Modeller 10.1 release
by Modeller Caretaker 18 Mar '21

18 Mar '21

A new version of Modeller, 10.1, 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 10.1 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.1 is a minor update that adds support for Apple Silicon. The Mac installer (dmg file) is now universal and will work on both Intel Macs and the new Apple Silicon (M1 or ARM64) Macs. The Homebrew Modeller package also works on both Intel and Apple Silicon Macs. If you encounter bugs in Modeller 10.1, please see https://salilab.org/modeller/10.1/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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query regarding alignment
by anuricha sharma 15 Mar '21

15 Mar '21

Hello sir, I have a query regarding the alignment, that how can I align my two pdb structures and one query sequence(xyz.ali) together using basic modelling, I am unable to to do alignment using two models and one query sequence in basic modelling as it aligns only one model and one query sequence, can you suggest any changes that I need to do in my align2d.py file. ReplyForward Sent from Mail for Windows 10

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can I add ambiguous restraints to modeller
by Li Xue 13 Mar '21

13 Mar '21

Hello all, Does modeller accept ambiguous restraints? For example, I know there is helix in a region but I am not sure where it starts. Best, Li

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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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