[log in to unmask] 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:[log in to unmask]] Im Auftrag
> von Tim Gruene
> Gesendet: Mittwoch, 15. April 2015 09:58
> An: [log in to unmask]
> 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: [log in to unmask]
phone : +49 0931 31 84031
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