<div dir="ltr">Adrian<div><br></div><div>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.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><font face="arial, sans-serif">Cheers</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Nigel</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">---</font></div><div><font face="arial, sans-serif">Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</font></div><div><font face="arial, sans-serif">Lawrence Berkeley National Laboratory</font><br><font face="arial, sans-serif">Berkeley, CA 94720-8235</font><br><font face="arial, sans-serif">Email : NWMoriarty@LBL.gov</font></div><div><font face="arial, sans-serif">Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></font></div></div><div><font face="arial, sans-serif"><span style="color:rgb(73,74,76)">ORCID : </span><font color="#494a4c"><a href="https://orcid.org/0000-0001-8857-9464" target="_blank">orcid.org/0000-0001-8857-9464</a></font></font><br></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Sep 19, 2023 at 7:12 PM Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Adrian,<br>
<br>
thanks for suggestions and comments.<br>
<br>
I hope Nigel can comment more, AFAIK making ReadySet mmCIF friendly is <br>
an on-going project and perhaps that won't happen before the upcoming <br>
release.<br>
<br>
The troubles you describe look a bit artificial to me. Here is why. <br>
First, mmCIF is now the only file format accepted by PDB for <br>
crystallographic depositions and AFAIK the same is about to happen for <br>
cryo-EM (if not happened already). So it may be a good idea to use mmCIF <br>
consistently. Second, adding H atoms seems more like a model building <br>
rather than refinement, so while it is possible of course to add them as <br>
part of a refinement run, it doesn't seem to be a huge deal adding them <br>
to your model once (once you are ready) and then keep from that point <br>
on. And, finally, it's been said here and elsewhere countless amount of <br>
times that adding H for refinement and then deleting them afterwards is <br>
not a good practice (to say the least).<br>
<br>
All the best!<br>
Pavel<br>
<br>
On 9/14/23 06:18, Adrián González López wrote:<br>
> Hi Phenix team,<br>
><br>
> I have a couple of feature suggestions:<br>
> 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.<br>
><br>
> Thanks!<br>
><br>
> Best,<br>
> Adrián<br>
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