Re: [phenixbb] (no subject)

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 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 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" 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:* [email protected] < [email protected]> on behalf of Ashok Nayak < [email protected]> *Sent:* Wednesday, November 18, 2015 7:58 AM *To:* [email protected] *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