[Chimera-users] one more question

[Elaine Meng]

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 at 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
>