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@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@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@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@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Ashok Nayak <ashokgocrackin@gmail.com>
Sent: Wednesday, November 18, 2015 7:58 AM
To: phenixbb@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