Hi Zhengzheng, I don’t know python either, but maybe you just need to get a newer Chimera. I tried the production release (1.13) and a recent daily build (1.14) and I did not see any error message when opening your PDB file. I do see some warnings in Reply Log (open from Favorites menu) like this: warning: cannot find LINK/SSBOND residue ZN (953 ) … but it is probably just because the header information in the first part of the file refers to the other chains that I assume you had deleted from the structure. In that case the warning messages are expected and could be ignored. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 7, 2018, at 7:58 PM, zheng l <zhengsfriend@hotmail.com> wrote:
Dear Dr. Meng.
Thank you so much for suggestion of add and delete H in the command line! This time it works for the structure modification!
I want to ask you one more question about an error that pop up every time i am trying to modify and I attached the error message above. (this is not a major issue but i just do not understand why it always show up whenever i set modification to the structure.)
I know the error is related to the Zn atom in the structure, but p53 sequence specific DNA binding domain does contain a Zn atom that binds 4 different amino acids.
I only know very little python and does not know where the error comes from.
May you please suggest why is Chimera not happy with the Zn atom in the structure?
Thank you! Zhengzheng