Dear Abhilash,
Starting May 3, 2022, the PDB archive distributes assembly files in
PDBx/mmCIF format. You can access the files here:
ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF/
Alternatively, you can use the PDBe download service:
https://www.ebi.ac.uk/pdbe/download/
You could retrieve th
Hello,
You can use phenix.fetch_pdb to get the files and
phenix.pdb.biomt_reconstruction command-line tools to get biological
assemblies. Depending on your need you can either go with bash/csh
scripting calling command-line tools or with python calling functions from
CCTBX. Let me know if you need
Dear Anton,
May I suggest that you contact the wwPDB directly through the
"Communication" tab of your deposition session? We'll then be able to
look at your files and advise you.
Kind regards,
Deborah
PDBe
On 18/07/2022 08:39, Anton Hamann wrote:
Hello
I'm having some trouble uploading t
Dear colleagues,
EMBL-EBI is looking to recruit a new Team Leader (EMBL Faculty position) to
take charge of the Electron Microscopy Data Bank (EMDB; emdb-empiar.org), one
of the three core archives of the Worldwide Protein Data Bank organisation
(wwPDB; wwpdb.org).
In the past two years, EMD
Hi All,
Our Formulatrix imager is nearing its end of life date and we are interested in
a suitable replacement. Anyone who has recently purchased a Formulatrix (or
similar) imager and who is willing to discuss their experience, please email me
directly.
Many thanks,
Jeff
Jeffrey B. Bonanno, P
As Refmac5.8.0349 is used, I am almost sure CCP4 8.0 is used. By the
way I would recommend to apply CCP4 update 002 (latest), as a LIBG
(base pair/stacking restraints) related bug was fixed in Refmac.
There might be something wrong with 4D4, but the problem is related to
OP3 atoms in nucleotides t
That is a strange case. Could you please check the monomer library version?
Especially, could you please check group name for 4D4, there seems to be a
confusion there.
Regards
Garib
> On 18 Jul 2022, at 09:28, Paul Emsley wrote:
>
> On 18/07/2022 07:59, Cryo EM wrote:
>> Hi all,
>>
>> I am w
On 18/07/2022 07:59, Cryo EM wrote:
Hi all,
I am working on a pdb of RNA where I intend to change the modified
nucleotides to their parent unmodified original residues. For example,
PSU to U, 1MG to G and so on.
I was wondering if there is a better way to do that by either manually
editing th
Hello
I'm having some trouble uploading the mmCIF files to the wwPDB_deposition from
PDB_Extract. The 2 errors are as follow:
Critical Data Values: Structure factor file is missing freeR set.
PDB format issues: Chain IDs contain more than one character.
How can I fix these errors?
Thank you for
