-
Notifications
You must be signed in to change notification settings - Fork 31
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
NQH-flipper #83
Comments
NQH-flipper itself is mostly Python scripts and it is not distributed under an open-source license, so there are technical and legal barriers for any kind of direct incorporation into MOPAC. I appreciate that rotamer analysis is a useful tool for protein structure refinement and analysis, but I'm not sure it belongs as a core feature of an electronic structure code, it is more of a type of workflow (hence its implementation w/ Python scripts) that organizes and post-processes a set of independent calculations (energetic tests of different rotamer assignments). It's something that I would be willing to try to make accessible as part of a Python interface to MOPAC, depending on the difficulty of implementation. Also, there are other tools besides NQH-flipper that list rotamer analysis among their features, such as Phenix. MOPAC doesn't really have the developer manpower right now to compete with the analysis tools of specialized protein refinement software like that with a large number of developers. |
I should ask for clarification: are you interested in constructing rotamers by selecting specific residues, or are you interested in automated selection of the "best" rotamer by some metric? I can probably support the former in MOPAC itself with its existing detection and bookkeeping of residues. It is the latter feature that would be quite difficult to incorporate directly into MOPAC. |
I would concur that Phenix (or maybe even cctbx) can do the NQH flips prior to running MOPAC. Molprobity with tell you all the side chains that need flipping. I redid the refinement with Phenix and A192 was corrected. |
Automated selection of the "best" rotamer would be the best approach |
As per Nigel's suggestion, there are several other tools for both constructing rotamers and guiding their selection. Since this discussion was last active, I also noticed that In your case, your notion of "best" rotamer may be different from other people with other applications, and so this must necessarily be part of a flexible/complicated workflow involving multiple tools and advanced user input and guidance. |
I would like to propose a feature to correct the rotamers, mainly asparagine, glutamine and histidines while working with protein models. Jimmy proposed the use of https://flipper.services.came.sbg.ac.at/cgi-bin/flipper.php but I think this feature should be included in this software to prevent user silliness/unawareness/ignorance/incompetence/uneducationess while working with these files by removing the possible distortion.
Please see http://openmopac.net/PM7_and_PM6-D3H4_accuracy/Notes_on_Proteins.html
The text was updated successfully, but these errors were encountered: