Hi,
External structure atomic bond distance restraints for use in refmac are
generated using ProSMART.
The webpage is here: http://www.ysbl.york.ac.uk/mxstat/Rob/index.html
Email me if you want a pre-release version.
Regards,
Rob
On 9 Jul 2011, at 18:00, Robbie Joosten wrote:
> Hi Qixu,
>
Hi,
I'm aware of two ways to do this:
by writing the colour as a word, e.g:
color white, (mypdbfile//A/*/*)
which will colour a whole chain.
Or by using rgb colours, e.g:
set_color newcolor0 = [1,1,1]; color newcolor0, (mypdbfile//A/2/*)
which will colour individual residues (residue 2 in this
Hi Petr,
Have you tried looking at the clashscore, and other statistics
provided by MolProbity? I think this is exactly what you're looking
for. It's a pretty good resource for ironing out errors during final
refinement stages: http://molprobity.biochem.duke.edu/
Regards,
Rob
On 27 Aug
Dear Xavier,
I recommend having a look at a few of the articles that were published
in the special issue of Acta Cryst D from June this year - Proceedings
of the third CCP-EM Spring Symposium.
https://journals.iucr.org/d/issues/2018/06/00/
Best regards,
Rob
-- Original Message --
I believe Julia is absolutely right.
The other consideration that I haven’t seen mentioned yet in this thread is the
effect on refinement. If you truncate a side chain or set it to zero occupancy
then the bulk solvent mask would contain that region that is actually occupied
by the flexible side
Dear Marian,
How do you know that it’s still a double bond? Is it due to the way that it’s
displayed in Coot, or based on the interatomic distances after refinement?
Could you have a look in the AceDRG link dictionary (.cif) and confirm the
order of the bond? Search for a “_chem_mod_bond” loop
r5021/index.html
https://journals.iucr.org/d/issues/2021/06/00/ir5022/index.html
Regards,
Rob
Dr Rob Nicholls
Senior Investigator Scientist
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH
> On 3 Jun 2021, at 19:10, Gerlind Sulzenbacher
.): Much better than my previous dinosaur approach.
> Thanks again and all the best,
> Gerlind
>
>
> On 03/06/2021 20:17, David Briggs wrote:
>> Hi Gerlind,
>>
>> Rob Nicholls gave a talk on how to deal with covalent linkages using AceDrg
>> at CCP4 stu
Dear Rens,
CCP4i2 now contains a CIF dictionary accumulator, which should help with
handling such problems (note it's also available as standalone to be used via
command line if that's useful). This is used automatically when providing
multiple ligand CIF dictionaries to the Refinement interfac
Hi Luca,
You should find that the hydrogens in the mmCIF file output by Refmac are
flagged as riding hydrogens, not as an explicit part of the model. This
behaviour is as intended, and should not pose a problem for deposition. They
are not in the output PDB file because there is no way to flag
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