Hi Tim,
While we did not make this information available yet, there is a way to get
"non-bonded clash score" that does take into account symmetry related clashes
using the Phenix command:
>>> phenix.pdb_interpretation .pdb nonbonded_clashscore=True
Testing for clashes is done in a slightl
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
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.
This brings me a related issue with COOT: the spherical refinement does
not consider symeqs either or does it?
Xavier
Original Message
Subject:Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?
Date: Thu, 23 Oct 2014 14:53:53 +0200
From: Jose Manuel
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] molprobity clashscore, symmetry-related molecules?
>
> Hi everybody,
> Molprobity does not take into account contacts/clashes from symmetry-
> related molecules, or does it?
> Thanks in advance,
> Tim
Molprobity does not look at contacts from symmetry partners, but only at
the asymmetric unit ones.
Unfortunately the clash scores in the PDB validation reports are based
on Molprobity and thus they won't count clashes outside the AU. See for
instance structures 4bmw or 1jkm. Both contain serio
on 23/10/14 11:52 AM, Tim 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 do
Hi everybody,
Molprobity does not take into account contacts/clashes from
symmetry-related molecules, or does it?
Thanks in advance,
Tim
Ok, I'm completed baffled... and have obviously started something
unintentionally...
NB: it was a joke!
I was amused that Molprobity, after 'adding' hydrogens to my model, had
'improved' the clashscore of my model by an obviously unnecessary number
of decimal places...!
[0.0098 point
On Thu, Jan 12, 2012 at 8:11 AM, Pavel Afonine wrote:
>
>> Who needs hydrogens?
>
>
> may be you need to read this (for example):
>
> http://www.phenix-online.org/papers/dz5209_reprint.pdf
>
While this reference is useful, it neglects the role of prior chemical
forces (vdW and electrostatics, fo
o:antony.oli...@sussex.ac.uk>>
Cc: mailto:CCP4BB@jiscmail.ac.uk>>
Subject: Re: [ccp4bb] Molprobity Clashscore
Tony,
Who needs hydrogens?
may be you need to read this (for example):
http://www.phenix-online.org/papers/dz5209_reprint.pdf
?
Pavel
Tony,
Who needs hydrogens?
>
may be you need to read this (for example):
http://www.phenix-online.org/papers/dz5209_reprint.pdf
?
Pavel
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