[Chimera-users] changing and saving structure

Elaine Meng meng at cgl.ucsf.edu
Mon May 2 09:44:55 PDT 2011

Dear Preetam,
My best guess is that you have not really changed the structure to remove clashes.

If you use the command ~findclash to remove clashes, that means only to remove the lines showing the clashes.  It does not change the structure.  

To change the structure so that it does not have clashes would require other actions that really change the coordinates, such as rotating bonds yourself, moving molecules or chains relative to one another, or performing energy-minimization.  When you save the PDB file, it will include any changes in coordinates you have made.

See this discussion on "modifying and saving data"  in Chimera, and its links:

The "structure analysis and comparison" tutorial also includes some clash detection and bond rotation:

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 2, 2011, at 5:15 AM, preetam nayak wrote:

> Respected sir,
>                    I am using chimera for the first time.I just want to ask that after successfully removing all clashes/contacts in my pdb file using commandline arguement  selectively,I am unable to save this modified pdb file even after trying many a times.Everytime I am saving my pdb file after modifications,the changes are not at all saved and again when I am opening the pdb file ,it is showing the same clashes/contacts.Sir,please help by providing the required steps as to how to save the changes one has made in the pdb file. 

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