Updating other tools to use and output in mmCIF format and option to add hydrogens in real_space_refine
Hi Phenix team, I have a couple of feature suggestions: It would be great if all the other tools within phenix would be able to have mmCIF files as both input and output. It causes a lot of problems when you are forced to switch between pdb and mmCIF, for example when using ReadySet to add hydrogens. On that note, it would also be very useful to have an option in real space refine to add hydrogens automatically before the refinement and remove them after the refinement. Thanks! Best, Adrián När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
Hi Adrian, thanks for suggestions and comments. I hope Nigel can comment more, AFAIK making ReadySet mmCIF friendly is an on-going project and perhaps that won't happen before the upcoming release. The troubles you describe look a bit artificial to me. Here is why. First, mmCIF is now the only file format accepted by PDB for crystallographic depositions and AFAIK the same is about to happen for cryo-EM (if not happened already). So it may be a good idea to use mmCIF consistently. Second, adding H atoms seems more like a model building rather than refinement, so while it is possible of course to add them as part of a refinement run, it doesn't seem to be a huge deal adding them to your model once (once you are ready) and then keep from that point on. And, finally, it's been said here and elsewhere countless amount of times that adding H for refinement and then deleting them afterwards is not a good practice (to say the least). All the best! Pavel On 9/14/23 06:18, Adrián González López wrote:
Hi Phenix team,
I have a couple of feature suggestions: It would be great if all the other tools within phenix would be able to have mmCIF files as both input and output. It causes a lot of problems when you are forced to switch between pdb and mmCIF, for example when using ReadySet to add hydrogens. On that note, it would also be very useful to have an option in real space refine to add hydrogens automatically before the refinement and remove them after the refinement.
Thanks!
Best, Adrián
Adrian
Pavel comments are correct. I can add that I have spent most of this week
getting the "ReadySet!-for-mmCIF" working. I am hoping for a release in the
near future.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : [email protected]
Web : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464
On Tue, Sep 19, 2023 at 7:12 PM Pavel Afonine
Hi Adrian,
thanks for suggestions and comments.
I hope Nigel can comment more, AFAIK making ReadySet mmCIF friendly is an on-going project and perhaps that won't happen before the upcoming release.
The troubles you describe look a bit artificial to me. Here is why. First, mmCIF is now the only file format accepted by PDB for crystallographic depositions and AFAIK the same is about to happen for cryo-EM (if not happened already). So it may be a good idea to use mmCIF consistently. Second, adding H atoms seems more like a model building rather than refinement, so while it is possible of course to add them as part of a refinement run, it doesn't seem to be a huge deal adding them to your model once (once you are ready) and then keep from that point on. And, finally, it's been said here and elsewhere countless amount of times that adding H for refinement and then deleting them afterwards is not a good practice (to say the least).
All the best! Pavel
Hi Phenix team,
I have a couple of feature suggestions: It would be great if all the other tools within phenix would be able to have mmCIF files as both input and output. It causes a lot of problems when you are forced to switch between pdb and mmCIF, for example when using ReadySet to add hydrogens. On that note, it would also be very useful to have an option in real space refine to add hydrogens automatically before
On 9/14/23 06:18, Adrián González López wrote: the refinement and remove them after the refinement.
Thanks!
Best, Adrián
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
participants (3)
-
Adrián González López -
Nigel Moriarty -
Pavel Afonine