<div dir="ltr">
<span></span>
<p style="margin-bottom:0in;line-height:100%;background:transparent">
So,
</p>
<p style="margin-bottom:0in;line-height:100%;background:transparent">Both the
phenix-generated mtz file (silly me for not checking this first) and
the cif file generated by <span lang="en-US">aB_deposition_combine
</span><span lang="en-US">can be uploaded on the PDB server.</span></p>
<p style="margin-bottom:0in;line-height:100%;background:transparent"><span lang="en-US">Thank
you all for your help!!</span></p>
<p style="margin-bottom:0in;line-height:100%;background:transparent"><span lang="en-US">Andrea</span></p>
</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Dec 17, 2022 at 5:06 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,<br>
<br>
two hopefully relevant points:<br>
<br>
- phenix.refine always produces an MTZ file that contains the copy of <br>
all inputs plus all is needed to run refinement (free-r flags, for <br>
example). So if you use that file for deposition you have all you need.<br>
<br>
- Unless there are strongly advocated reasons to do otherwise in your <br>
particular case, you better use in refinement and deposit the original <br>
data and NOT the one touched by any of available these days magic sticks <br>
(that "correct" for anisotropy, sharpen or else!).<br>
<br>
Other comments:<br>
<br>
> - However, CCP41/Refmac5 does not (yet) read .cif reflection files. As <br>
> far as I know, Phenix Refine does not (yet) neither.<br>
<br>
Phenix supports complete input / outputs of mmcif/cif format. For <br>
example, phenix.refine can read/write model and reflection data in cif <br>
format. It's been this way for a long time now.<br>
<br>
Pavel<br>
<br>
<br>
On 12/16/22 17:32, Andrea Piserchio wrote:<br>
> Dear all,<br>
><br>
><br>
> I am trying to validate and then (hopefully) deposit a structure <br>
> generated using the autoproc/staraniso staraniso_alldata-unique.mtz <br>
> file as input for phenix.refine.<br>
><br>
> Autoproc also produces a cif file ( Data_1_autoPROC_STARANISO_all.cif) <br>
> specifically for deposition.<br>
><br>
> Long story short, the PDB validation server complains about the lack <br>
> of a freeR set for both files. I realized that, at least for the cif <br>
> file, the r_free_flag is missing (but why does the .mtz for the <br>
> isotropic dataset work??),so I then tried to use for validation the <br>
> *.reflections.cif file that can be generated by phenix.refine. This <br>
> file can actually produce a validation report, but I still have some <br>
> questions:<br>
><br>
> 1) Is it proper to use the .reflections.cif file for this purpose? <br>
> During the upload I do see some errors (see pics); also, the final <br>
> results show various RSRZ outliers in regions of the structure that <br>
> look reasonably good by looking at the maps on coot, which seems odd ...<br>
><br>
> 2) In case the *.reflections.cif is not adequate/sufficient for <br>
> deposition (I sent an inquiry to the PDB, but they did not respond <br>
> yet), can I just add a _refln.status column to the autoproc cif file <br>
> (within the loop containing the r_free_flag) where I insert “f” for <br>
> r_free_flag = 0 and “o” everywhere else?<br>
><br>
><br>
> Thank you in advance,<br>
><br>
><br>
> Andrea<br>
><br>
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</blockquote></div>