, October 21, 2010 5:05 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Regarding space group P1, P21
There is nothing fundamentally wrong with refining in P1 even if the
P21212 symmetry is present. An effective way to reduce the number of
parameters wold be to introduce tight restraints. If you
[...@mrc-lmb.cam.ac.uk]
Sent: Thursday, October 21, 2010 9:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Regarding space group P1, P21
It's more complicated than that, since the tricky thing is to distinguish
between reflections related eg by a putative crystallographic two-fold
Dear CCP4BB members,
I have solved a protein-drug complex structure in P21212 space group. In this
structure, the drug molecule is falling on the two-fold symmetry axis having
averaged electron density with 0.5 occupancy. We tried a lot to crystallize
this protein-drug complex in different
Hi
Since you're using iMosflm to process the data, it is well worthwhile running
the Quickscale task following integration (I would actually run it after
integrating ~5 - 10 degrees of data) to see if the true crystal symmetry
determined by analysing agreement of the intensities of symmetry
There is nothing fundamentally wrong with refining in P1 even if the
P21212 symmetry is present. An effective way to reduce the number of
parameters wold be to introduce tight restraints. If you decide to
lower the symmetry, go with P21 as it still keeps your ligand off
symmetry axes. You can
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Regarding space group P1, P21
There is nothing fundamentally wrong with refining in P1 even if the
P21212 symmetry is present. An effective way to reduce the number of
parameters wold be to introduce tight restraints. If you decide to
lower the symmetry, go with P21
Dear Mohinder,
On Thu, Oct 21, 2010 at 01:05:42PM +0100, Mohinder Pal wrote:
The question is , is it a good practice to solve this structure in
P1 and P21 even if the data has higher symmetry?
On a slightly philosophical note regarding the final model (and not
necessarily the 'good practice'
Hi Herman,
On Thu, Oct 21, 2010 at 05:31:51PM +0200, herman.schreu...@sanofi-aventis.com
wrote:
If you process your data in a lower symmetry space group, you will have
more unique reflections, since reflections which are related by the
higher symmetry will be avaraged during scaling in a
*From:* Mohinder Pal m...@soton.ac.uk
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Thu, October 21, 2010 7:05:42 AM
*Subject:* [ccp4bb] Regarding space group P1, P21
Dear CCP4BB members,
I have solved a protein-drug complex structure in P21212 space group.
In this structure, the drug molecule
From: Mohinder Pal m...@soton.ac.uk
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thu, October 21, 2010 7:05:42 AM
Subject: [ccp4bb] Regarding space group P1, P21
Dear CCP4BB members,
I have solved a protein-drug complex
@JISCMAIL.AC.UK
Sent: Thursday, October 21, 2010 10:55 AM
Subject: Re: [ccp4bb] Regarding space group P1, P21
You pick the Rfree flags in the high-symmetry space group, and then use CAD with
OUTLIM SPACE P1 to
symmetry-expand them to P1 (or whatever you like).
Things get trickier, however, when your NCS
- Original Message -
From: James Holton
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, October 21, 2010 10:55 AM
Subject: Re: [ccp4bb] Regarding space group P1, P21
You pick the Rfree flags in the high-symmetry space
The black eye comes not from the treatment of the observations, but from
the
treatment of the model. If you want to refine the same model against
lower
symmetry and/or unmerged data - go right ahead. I think the result will
not
usually be an improvement, but in some cases this may work around
Hi Ed,
On Thu, Oct 21, 2010 at 12:18:31PM -0400, Ed Pozharski wrote:
Let's say I have a ligand on symmetry axes and so it appears in two
conformations. If I reduce symmetry, there are two possible scenarios.
a. In lower symmetry, ligand still appears in two conformations. Shall
use higher
On Thu, 2010-10-21 at 12:58 -0500, Jacob Keller wrote:
On the other hand, if somehow a few sidechains became systematically
different between molecules in the p1 cell, it *would* make sense to
refine
in p1
And sometimes (but rarely) such differences become detectable at high
resolution
Hi,
I think that when you say as if they were independent, you are begging
the question. You could say that refining in higher symmetry treats the
molecules as if they were the same. Further, it really assumes more to
posit that they are the same.
But we're still talking about crystals,
On Thu, 2010-10-21 at 18:59 +0100, Clemens Vonrhein wrote:
I think I understand what you're getting at: you have a lower symmetry
with a NCS axis that is basically perfectly aligned with the
corresponding crystallographic axis in the higher symmetry
spacegroup. And the only part of the model
But we're still talking about crystals, right? The whole reason for
trying to crystallise our proteins/DNA/RNA is because we ideally want
a perfect arrangement of molecules. So taking as a starting hypotheses
the conservative approach that if the data really looks like P21 it
probably is P21
Hi Clemens,
Sorry to be picky and start the 'definition game' over again, but
'Miller indices' are strictly not the numbers that index X-ray
reflections that everyone is familiar with (whether observed or not!).
Miller indices were introduced in 1839 by the British mineralogist
William Hallowes
:00 PM
Subject: Re: [ccp4bb] Regarding space group P1, P21
Hi Clemens,
Sorry to be picky and start the 'definition game' over again, but
'Miller indices' are strictly not the numbers that index X-ray
reflections that everyone is familiar with (whether observed or not!).
Miller indices were
On Thursday, October 21, 2010 11:38:55 am Jacob Keller wrote:
if the data really looks like P21-- what are the criteria for that?
This is a straightforward statistical question.
In testing for a possible 2-fold, you want to know:
Do two random reflections related by the putative 2-fold
It's more complicated than that, since the tricky thing is to distinguish
between reflections related eg by a putative crystallographic two-fold and by a
parallel non-crystallographic two-fold, which would give very similar intensity
relationships. Pointless does try to score these alternative
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