The CCP4 Study Weekend (7 - 9 January 2015)
East Midlands Conference Centre, University of Nottingham
Wednesday 7 - MX User Meeting
Thursday 8 / Friday 9 - CCP4 Study Weekend
Advances in Experimental Phasing
We cordially invite you to participate in this year's Study Weekend at the the
East
*/Postdoctoral position in protein biochemistry/molecular biology/*
A senior postdoctoral position is available to work on peptidases, their
inhibitors and their complexes. The hosting place is the
Proteolysis Lab of the Molecular Biology Institute of Barcelona (IBMB)
from the Spanish Research
Does anyone know if Molprobity has recently changed the standard bond lengths
and angles that it uses ?
Molprobity is reporting errors in the C4-C5 bond length and the C5-C4-N3 bond
angle (deviations of 8-10 sigma) for AMPPNP (monomer code ANP) for a new
structure refined with Refmac. I then
I want to have a quantitative estimate for the accessible solvent area for a
Selenocysteine residue in a tripeptide, gly-Sec-gly. AreaImol doesn't recognize
Selenium, at least in the version I'm using (6.1.1). The online documentation
for Areaimol doesn't include the text Selenium. Do newer
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Hi Andrew,
the ccp4 ANP.cif entry for C4'-C5' is 1.528A, but both the Phenix and
Grade cif list 1.508A. The distance in 2JDI is 1.53, so if molprobity
relies on one of the latter two sources, this might be the source of the
flag. Also some shelxl dictionary lists 1.509A, so it's 3:1 for the flag
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In general the word outlier should not be read as error. It
simply means that this thing is interesting. You have to judge, based
on all information at hand, if it is interesting because it is rare or
because it is wrong.
It is true that the
On 15 Sep 2014, at 15:24, Andrew Leslie and...@mrc-lmb.cam.ac.uk wrote:
This would suggest that the standard dictionary that Molprobity uses has
changed, but I cannot find any reference to this on the Molprobity pages.
I would be very grateful if anyone can
Dear Huw,
Many thanks for this information. I had seen the notice about Molprobity using
CCTBX validation metrics, but I mistakenly thought that Phenix used the CCP4
monomer library, which I think was true once but is clearly no longer the case.
Given the very small sigma values associated
Andrew, GRADE gives:
ANP C5 C4aromatic 1.388 0.011
ANP C5 C4 C3 126.8 0.7
i.e. essentially the same as Phenix, so I would go with that.
The CCP4 values definitely could do with a re-examination: I've never heard
of a double bond with a length of 1.49, and
On 15/09/14 18:05, Dale Tronrud wrote:
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On 9/15/2014 9:42 AM, Andrew Leslie wrote:
Dear Huw,
Many thanks for this information. I had seen the notice about
Molprobity using CCTBX validation metrics, but I mistakenly thought
that Phenix used the
Forgot the picture! Here is it!
From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk]
Sent: Sunday, September 14, 2014 6:16 PM
To: Wang, Bing
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ligand mismathces in pdb deposit
On 12/09/14 23:28, Wang, Bing wrote:
Hi
Hi Bing,
This is the result of the new PDB deposition system being buggy. I had a
similar problem with imidazole recently. This is the solution given to me
by the PDB annotators.
Please choose from the instance page:
type of ligand: heterogen,
then give alternate ligand ID as IMD, (in your
On 15 September 2014 17:48, Ian Tickle ianj...@gmail.com wrote:
ANP C5 C4 C3 126.8 0.7
Oops sorry, typo:
ANP C5 C4 N3 126.8 0.7
I.
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