[phenixbb] Updating other tools to use and output in mmCIF format and option to add hydrogens in real_space_refine

[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

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