Hello all,
MolProbity person here. I am not a regular reader of the CCP4 Bulletin
Board, but I see there were some recent questions about MolProbity's status.
The MolProbity webserver occasionally encounters jobs that hang and prevent
new job submissions. That is likely what caused the recent M
Hi All,
I hope this is the right place to ask about this.
I have tried to use a local installation of molprobity to run batches of files
and I get these errors:
clashscore test.pdb
Warning: ini_set(): Headers already sent. You cannot change the session
module's ini settings at this time in
Seems to be working fine:
https://downforeveryoneorjustme.com/molprobity.biochem.duke.edu. It's
not a secure site, though: https://molprobity... times out, whereas
http://molprobity... goes through. Could that be your issue?
On 2019-06-04 13:19, Andrea Pica wrote:
Hi everyone,
it seems that
Hi everyone,
it seems that MolProbity website (molprobity.biochem.duke.edu) is not
reachable.
Anyone knows what happened?
Cheers,
Andrea
--
Andrea Pica. Ph.D.
Postdoctoral Researcher
High-Throughput Crystallization Lab
EMBL Grenoble Outstation
Postal address: European Molecular Biology Lab
Hi Nick,
thanks for your report; I'm on it.
Cheers,
Jon
On Fri, 29 Mar 2019 at 12:18, Nicholas Keep
wrote:
> I have found a 'feature' in molprobity. if there are two atoms on top
> of each other (not hard to do by mistake when adding waters in coot),
> then molprobity does not work or at leas
I have found a 'feature' in molprobity. if there are two atoms on top
of each other (not hard to do by mistake when adding waters in coot),
then molprobity does not work or at least does not give the outputs
required to then give the coot molprobity checklist file our of the
ccp4i2 refmac inte
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
It works now. Thanks for fixing.
Sincerely,SDY
Date: Mon, 11 Nov 2013 16:13:52 +
From: tanne...@missouri.edu
Subject: [ccp4bb] molprobity
To: CCP4BB@JISCMAIL.AC.UK
I encountered the same problem last night. The server won't upload the PDB
file. I didn't check this morning
I encountered the same problem last night. The server won't upload the PDB
file. I didn't check this morning.
On Nov 11, 2013, at 10:02 AM, SD Y wrote:
Hi,
I was wondering if molprobity server is down
(http://molprobity.biochem.duke.edu/index.php) or its just my files or our
network has p
Hi,
I was wondering if molprobity server is down
(http://molprobity.biochem.duke.edu/index.php) or its just my files or our
network has problem because I cant upload my files (some times it gave error).
ThanksSDY
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
Hello Rongjin Guan,
your problem most likely comes from different pdb version formats. The
files which work are probably pre pdb v. 3.0. Although (Win)Coot is
mainly v. 3 compliant here we are not (really (*)). A fix (at least for
the files which are not working) may be to change two lines (1
Hello,
I just installed Wincoot 0.6.1 and reduce/probe as well, and tested with
several
PDB files for probe/clash validation.
For some PDBs it worked perfectly; but for my own model, it did not work and I
have
the following message:
.
Found 0 hydrogens (0 hets)
S
Hi everyone:
I am trying to reduce my clashscore in Coot using Molprobity. I can get the
dots to display alright, but they do not update when I change the
rotamer/angles. Here's my .coot
(define *probe-command*
"/gdata1/deacona/molprobity/molprobity3/bin/linux/probe")
(define *reduce-command*
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