See here for definition of polar point group:
http://pd.chem.ucl.ac.uk/pdnn/symm2/polar1.htm .
SG P321 is in PG 32 which has a unique point where the axes intersect so is
not polar.
Note that non-centrosymmetric non-enantiomorphic PGs m, mm2, 3m, 4mm and
6mm are also polar, so it's not just
Hi Natalia,
As this is not a phenix-specific question I'll answer here on the CCP4 bulletin
board (for questions that are just for phenix it is best to use the phenix
mailing list instead).
Your heavy atom sites (and your protein molecule) are repeated millions of
times throughout your
Dear CCP4bb,
When we select 'generate all hydrogen atoms' option in Refmac5, does it use
riding hydrogen model in refinement?
--
Regards,
Sasha Pausch
Hi Sasha,
Yes, it does and I highly recommend using this option all the time. It really
makes the VdW restraints much more effective.
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Sasha Pausch
Sent: Wednesday, April 15, 2015
Hi Bernhard, thanks for the pointer. It looks like most of the coot ncs
functions don't print the matrix values, which made exporting them tricky,
especially because I'm pretty new to scripting in Python.
I have 4 chains, and
ncs_ghosts(0) just spits out
result is [['NCS found from matching
good enough to pass the orthonormal test.
.. scratch that, it passes sometimes and still fails for other
structures/chains. So I'm still in search of a higher-precision export
Shane
On Wed, Apr 15, 2015 at 11:44 AM, Shane Caldwell shane.caldwel...@gmail.com
wrote:
Hi Bernhard, thanks for
Dear Shane,
It's not CCP4, but Tom Terwilliger's find_ncs program works conveniently. Like
coot, it's only returning 4 decimal places, if that's a problem (though adding
a 5th decimal place would only typically change the result of a rotation by
hundredths of an Angstrom). I've just tried
Hi again ccp4bb. Thanks for your help and sorry for the spam! I've chased
down the variables and figured out how to export them as full floats with a
simple print command. I'll put together a script for anyone who wants to do
so in the future.
Cheers,
Shane
On Wed, Apr 15, 2015 at 12:21 PM,
Dear All,
Thanks to everybody who answered my previous question about heavy atoms! I
got it now.
I have some more questions now.
1) I built a loop in Coot, right now it is a separate molecule. I also know
that it is possible to merge molecules, but if I do so, I’ll get my loop
connected to my
Hi all,
A little off-topic: I am beginning a post-doc in a non-crystallography lab
in a month, and I am working to get a list together of screens to purchase
before I arrive. Can anyone recommend screens for crystallizing antibodies
(Fab fragments), and Fab-antigen complexes?
Thanks,
-Jarrod
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Dear Chris,
did you check the map looks like what you expect it to be? If I remember
correctly, I had difficulties covering the Tl+/K+ ions from these data
because they lie at the very edge of the asymmetric unit. I used mapmask
as in the attached
Dear Gaoyina,
I agree with Thassos that it is unlikely that your cell axes are all 90 Å long
and more likely that you mentioned the angles. I also agree with Thassos that
it would be best to run Pointless or Xtriage.
However, I think it is also good to try to determine the space group
On 15 Apr 2015, at 7:55, 高艺娜 gaoy...@cau.edu.cn wrote:
Dear all,
Recentely I have got a dataset of 3.0A resolution and I have a big problem in
choosing space group because the crystal were found in both P4,P1and P222
space groups,here are the figures of self rotation function on P4,P1
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Dear Natalia,
you can use Coot to generate the symmetry related molecules and see if
the substructure matches your model.
If your space group is polar, as in e.g. P2(1) or P2(1)2(1)2(1), your
coordinates may float freely along the polar axis and
herman.schreu...@sanofi.com wrote:
Polar space groups have none or a single rotation axis, e.g. P1,
P2x, P3x, P4x, P6x. Otherwise Tims argument is valid.
Dear Herman,
Is there really a general definition what a 'polar space group' is?
For example, SG P321 would have more than a single
Dear Natalia,
First a quick correction to avoid confusion: P2(1)2(1)2(1) is not polar. Polar
space groups have none or a single rotation axis, e.g. P1, P2x, P3x, P4x, P6x.
Otherwise Tims argument is valid.
In coot, I would switch on symmetry and use a fairly large box and see whether
Dear Colleagues,
An opportunity exists at Synchrotron SOLEIL for an engineer or scientist to
develop the MXCuBE experimental control interface for the two MX beamlines,
PROXIMA 1 and PROXIMA 2A . The position is for a fixed term of 18 months
working on site with a group of motived scientists.
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