Dear Stephen,
The current monomer library is, for the most part, generated
by running AceDRG - for non-metal containing entries at least.
AceDRG [1,2] derives atom types using the cif files in the
Crystallography Open Database [3], not the CSD.
You can see which version of Acedrg has been using by examing the
_pdbx_chem_comp_description_generator block in the cif file.
[1] Fei Long, Robert A Nicholls, Paul Emsley, Saulius Gražulis, Andrius
Merkys, Antanas Vaitkus and Garib N Murshudov "ACEDRG: A stereo-chemical
description generator for ligands" Acta Cryst. (2017), D73, 112-122.
[2] Fei Long, Robert A Nicholls, Paul Emsley, Saulius Gražulis, Andrius
Merkys, Antanas Vaitkus and Garib N Murshudov "Validation and extraction
of stereochemical information fromsmall molecular databases" Acta Cryst.
(2017), D73, 103-111
[3] Gražulis, S., Chateigner, D., Downs, R. T., Yokochi, A. F. T.,
Quirós, M., Lutterotti, L., Manakova, E., Butkus, J., Moeck, P. & Le
Bail, A. "Crystallography Open Database (COD): an open-access collection
of crystal structures and platform for world-wide collaboration" J.
Appl. Cryst. (2009) 42, 726–729.
Best regards
Lucrezia
On 2022-11-28 17:29, stephen.c...@rc-harwell.ac.uk wrote:
Dear CCPBB,
I have a question regarding the origin of the monomer libraries in
CCP4. I ask because I have quoted the bond length listed in the
monomer library describing peroxide in a manuscript and a referee has
asked for a reference since they seem to disagree with the quoted
value of ~1.48 A. My understanding is that parameters describing bond
length, angles etc are derived from structures in the CSD is this the
case? Is there an appropriate reference out there somewhere?
Thanks very much in advance,
Steve
Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717
This email and any attachments may contain confidential, copyrightand
or privileged material, and are for the use of the intended addressee
only. If you are not the intended addressee or an authorized recipient
of the addressee, please notify us of receipt by returning the e-mail
and do not use, copy, retain, distribute or disclose the information
in or attached to this email.
Any views or opinions presented are solely those of the author and do
not necessarily represent those of the Research Complex at Harwell.
There is no guarantee that this email or any attachments are free from
viruses and we cannot accept liability for any damage which you may
sustain as a result of software viruses which may be transmitted in or
with the message.
We use an electronic filing system. Please send electronic versions of
documents, unless paper is specifically requested.
This email may have a protective marking, for an explanation, please
see:
http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.
-------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
