Dear Nadir and all,
I would expect that the developers of Molprobity possess sufficient
crystallographic knowledge to implement distance calculations in
crystallographic space rather than Euclidean space, and it is more
efficient to implement the handful lines of codes than to expect every
user to fiddle with their PDB-files.
It is not a lot to ask for.
Best,
Tim
On 10/24/2014 09:31 PM, Nadir T. Mrabet wrote:
> MolProbity works on chains present in the pdb file.
> Therefore, I would predict that if the pdb file can be made to consist
> of several chains (built by symmetry operations) and bearing each a
> distinct chain name, then MolProbity would (artificially) work on
> symmetry-related molecules as well.
>
> Nadir
>
> Pr. Nadir T. Mrabet
> Structural & Molecular Biochemistry
> N-gere - INSERM U-954
> University of Lorraine, Nancy
> School of Sciences and Technologies
> & School of Medicine
> 9, Avenue de la Foret de Haye, BP 184
> 54505 Vandoeuvre-les-Nancy Cedex
> France
> Phone: +33 (0)3.83.68.32.73
> Fax: +33 (0)3.83.68.32.79
> E-mail: Nadir.Mrabet <at> univ-lorraine.fr
> Cell.: +33 (0)6.11.35.69.09
>
> LEGAL NOTICE
> Unless expressly stated otherwise, this message is confidential and may
> be privileged. It is intended for the addressee(s) only.
> Access to this E-mail by anyone else is unauthorized.
> If you are not an addressee, any disclosure or copying of the contents
> of this E-mail, or any action taken (or not taken) in reliance on it,
> is unauthorized and may be unlawful.
> If you are not an addressee, please inform the sender immediately.
>
> On 23/10/2014 13:06, "Oliver Smart" wrote:
>> on 23/10/14 11:52 AM, Tim <[log in to unmask]> wrote:
>>
>>> Hi everybody,
>>> Molprobity does not take into account contacts/clashes from
>>> symmetry-related molecules, or does it?
>>> Thanks in advance,
>>> Tim
>>>
>> Tim,
>>
>> I am not sure. In my experience MolProbity reduce does not take crystal
>> contacts
>> into account (but reduce does a great job otherwise). But this might have
>> been improved.
>>
>> Oliver
>> -----------------
>> Dr Oliver Smart
>>
>> Director SmartSci Limited http://www.smartsci.uk/
>> & Consultant Global Phasing Ltd http://www.globalphasing.com/
>>
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
|