[phenixbb] (no subject)

Ashok Nayak ashokgocrackin at gmail.com
Wed Nov 18 21:09:56 PST 2015


Dear luzuok,
The merging job can easily be done in Pymol.
1.Create symmetry molecules (say at 4A radius) -> Select the symmetry
related molecules of your choice -> save the selected coordinates of the
same
 or
2.You can also do the same by saving the coordinates of two symmetry
related molecules separately and merge in a text file with proper TER
records.

regards
Ashok
CSIR-CDRI
Lucknow, INDIA

On Wed, Nov 18, 2015 at 9:09 PM, Ashok Nayak <ashokgocrackin at gmail.com>
wrote:

> Dear luzuok,
> The merging job can easily be done in Pymol.
> 1.Create symmetry molecules (say at 4A radius) -> Select the symmetry
> related molecules of your choice -> save the selected coordinates of the
> same
>  or
> 2.You can also do the same by saving the coordinates of two symmetry
> related molecules separately and merge in a text file with proper TER
> records.
>
> regards
> Ashok
> CSIR-CDRI
> Lucknow, INDIA
>
> On Wed, Nov 18, 2015 at 5:59 PM, luzuok <luzuokun at 126.com> wrote:
>
>> Dear Tom,
>> I have the same question too.
>> Another simple question is that how can I merge two symmetry related
>> molecule? Though I can  easily expand them by coot.
>>
>> Best!
>> Lu
>>
>>
>> --
>>
>>
>> Lu Zuokun, Ph.D. Candidate
>> College of Life Science, Nankai University
>>
>> 在 2015-11-18 23:14:48,"Terwilliger, Thomas Charles" <terwilliger at lanl.gov>
>> 写道:
>>
>> Hi Ashok,
>>
>> If you have a PDB file with 2 crystallographically-related copies of your
>> molecule, with one called chain A and one called chain B, you can run
>> phenix.simple_ncs_from_pdb on your PDB file to find the matrices and
>> translations.  Let me know if that doesn't do it!
>>
>> All the best,
>>
>> Tom T
>>
>>
>> ------------------------------
>> *From:* phenixbb-bounces at phenix-online.org <
>> phenixbb-bounces at phenix-online.org> on behalf of Ashok Nayak <
>> ashokgocrackin at gmail.com>
>> *Sent:* Wednesday, November 18, 2015 7:58 AM
>> *To:* phenixbb at phenix-online.org
>> *Subject:* [phenixbb] (no subject)
>>
>> Hello Phenix BB,
>> Like every amateur crystallographer I could easily generate symmetry
>> mates in a given radius in coot, but I wondered always which is the
>> crystallographic two fold axis axis(my space group being C2) through which
>> the molecule is rotated and translated (if it is) to get the next molecule.
>> I tried superpose to find the answer, but could only get the Euler angles
>> and transformation matrix and not the axis. Are there any programs where I
>> can get to know this, would be grateful to be enlightened for the same
>>
>> thanks BB in advance
>>
>>
>>
>> regards
>>
>> --
>> Ashok Nayak
>> PhD student-
>> Molecular and Structural Biology Division
>> CSIR-CDRI, Janakipuram Extension
>> Lucknow-226031
>> India
>>
>>
>>
>>
>>
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>
>
>
> --
> Ashok
> Senior Research Fellow - Dr JV Pratap, Lab No-LSN 008
> Molecular and Structural Biology Division
> Central Drug Research Institute, Janakipuram Extension
> Lucknow-226031
> India
>



-- 
Ashok
Senior Research Fellow - Dr JV Pratap, Lab No-LSN 008
Molecular and Structural Biology Division
Central Drug Research Institute, Janakipuram Extension
Lucknow-226031
India
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