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 rotation axis but
it would be polar along its twofolds, wouldn't it?
Best,
Clemens
In coot, I would switch on symmetry and use a fairly large box and
see whether symmetry atoms match your built molecule. In that case,
coot has options to write out the symmetry molecule. If not,
different origins might have been used, or a polar shift has to be
applied. In this case, you might try to manually superimpose your
Selenium coordinate using to Rotate Translate Zone option. By
careful only to translate, not to rotate.
Best,
Herman
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
von Tim Gruene
Gesendet: Mittwoch, 15. April 2015 09:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Phenix: heavy atoms
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 looking
the the symmetry related atoms would not help. I am not sure Coot
has a feature to drag the coordinates along the polar axis.
Best,
Tim
On 04/15/2015 05:24 AM, Natalia O wrote:
Dear All,
I am new to the crystallography and I am seeking for an advice
considering data processing. I have a dataset with 2.8 A resolution. I
used hybrid substructure search program in phenix, I got the heavy
atom sites (selenium), and then I submitted the site to the autosol.
With autosol half of the residues were positioned and there are some
loops missing, and a part of structure was built as a chain of
alanines. Importantly only half of the methionines was built. Now I am
trying to build loops manually in Coot. I was able to build one of the
loops, and this loop has a methionine residue, so I wanted to check if
one of the heavy atom sites agrees with the self-built methionine
position. And here I got completely confused, because if I open a pdb
file containing my heavy atom sites and at the same time I open the
model - the coordinates, they are not placed in one asymmetric unit. I
expected that heavy atoms were found, and then basically “on top of
them” the model was built. But that’s not what I see. I am missing
something basic and important here and I am completely clueless. What
is the relation between the origin of coordinates in the file with
heavy atoms and the origin of coordinates of the molecular model?
Thank you!
Natalia
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149
GPG Key ID = A46BEE1A
--------------------------------------------------
Dr. Clemens Grimm
Institut für Biochemie
Biozentrum der Universität Würzburg
Am Hubland
D-97074 Würzburg
Germany
e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
phone : +49 0931 31 84031
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