[phenixbb] mmCIF in Phenix 1.14-3260
osobolev at lbl.gov
Wed Dec 19 12:12:19 PST 2018
Unfortunately, we were not able to figure out the reason PDB not handling
Phenix mmCIFs. What is exact error message you are getting? Since the 1.14
release we changed some output to be more compliant with PDB mmCIF, so
there is a chance it will work with the latest nightly. Please keep
On Tue, Dec 18, 2018 at 10:23 PM Xavier Brazzolotto <
xavier.brazzolotto at chemdef.fr> wrote:
> Dear Oleg,
> I had the same issue lately (mmCIF not handled by PDB deposition system
> using Phenix 1.14.3260).
> Is this issue has been resolved in a recent nightly ?
> Many thanks
> Le 29 nov. 2018 à 20:20, Oleg Sobolev <osobolev at lbl.gov> a écrit :
> Dear Dominik,
> Thank you for letting us know!
> Would it be possible to send me (off-list) the 1.13 and 1.14 cif files for
> investigation along with the pdb file used for conversion. Also PDB
> deposition message would be helpful (if available). All files will be kept
> Best regards,
> Oleg Sobolev.
> On Thu, Nov 29, 2018 at 2:17 AM Dominik Oberthuer <
> dominik.oberthuer at desy.de> wrote:
>> Dear all,
>> I recently found that phenix.refine in version 1.14-3260 generates
>> coordinate mmCIFs that the PDB deposition system can't handle.
>> After struggling with this for some time I used an installation of
>> Phenix 1.13-2998 I still have on my MacBook and used the
>> mmCIF/PDB-conversion tool from this version and had no more trouble with
>> uploading the mmCIF to the PDB.
>> Maybe it is worthwhile to check which changes from 1.13 to 1.14 might
>> have caused these issues.
>> Dr. Dominik Oberthür
>> CFEL - Center for Free-Electron Laser Science - DESY
>> Coherent Imaging Division
>> Notkestrasse 85
>> 22607 Hamburg
>> phone: +49 (0)40 8998 6394
>> dominik.oberthuer at cfel.de
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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> Xavier Brazzolotto, PhD
> xavier.brazzolotto at chemdef.fr
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