Dear Bernhard,
The ideal and model coordinate files are generated using the
information available in the wwPDB Chemical Component cif files. The
"model" coordinate are from the PDB structure that has the first
instance of the ligand while the "ideal" coordinates are generated using
Molecular Networks' Corina, and if there are issues, OpenEye's OMEGA. It
appears that in the case of the ligands you have listed (and there are
500 other CCD files) there was issue with generating ideal coordinates
and in the export the coordinates are set to zero as was pointed out by
Tristan. We are investigating the issue of missing ideal coordinates
further.
Hope this explains the issue with the coordinate files.
Kind regards,
Sameer
On 2021-02-06 14:54, Bernhard Rupp wrote:
True. Sameer seems to be on it. In the meantime, I simly adjust my
expectations of 'ideal' :-)
Cheers br
On Sat, Feb 6, 2021, 06:40 Tristan Croll <[email protected]> wrote:
I know 🙂. Just suggesting the most likely cause of the problem.
-- T
-------------------------
From: Bernhard Rupp <[email protected]>
Sent: 06 February 2021 14:38
To: Tristan Croll <[email protected]>
Cc: [email protected] <[email protected]>
Subject: Re: [ccp4bb] ideal ligands
That is what 'uranium atom solution' implies:
All atoms collapsing into one :-)
Cheers br
On Sat, Feb 6, 2021, 06:34 Tristan Croll <[email protected]> wrote:
The ideal coordinates in the CCD entries for BCR and LUT are null
- my guess is that in these cases all the coordinates just default
to (0,0,0) in the PDBeChem script.
-------------------------
From: CCP4 bulletin board <[email protected]> on behalf of
Bernhard Rupp <[email protected]>
Sent: 05 February 2021 20:51
To: [email protected] <[email protected]>
Subject: [ccp4bb] ideal ligands
Hi Fellows,
PDBeChem under ‘ideal’ coordinates returns a small molecule
uranium atom solution for BCR, LUT, and possibly other
xanthophylls, eg.
ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/B/BCR/BCR_ideal.pdb
while the representative files are ok.
Is this intended?
Thx, BR
------------------------------------------------------
Bernhard Rupp
http://www.hofkristallamt.org/ [1]
[email protected]
+1 925 209 7429
+43 676 571 0536
------------------------------------------------------
Many plausible ideas vanish
at the presence of thought
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