Hi Zhengzheng The format of your PDB file is not standard because all the H atoms are all at the end instead of with their their residues. Also they are all in a different chain (chain A) than the other atoms (chain B). Whatever program wrote this file wrote it incorrectly. You can easily see all atoms, e.g. commands: ~ribbon display (or use Actions menu to do the same things) but if you use Chimera features requiring chemical knowledge (findhbond etc.) it will not work correctly if the H and the other atoms are not recognized as being in the same residue. I tried editing so that all atoms were chain B, but it did not fix the problem, which is apparently instead caused by placing all the H atoms at the end instead of with their individual residues. You could fix it be removing and re-adding hydrogens in Chimera, but then the H atom positions wouldn’t be exactly the same. Commands: delete H addh It is recommended to send questions to chimera-users@cgl.ucsf.edu (CC’ed here) in case I’m not available to answer. 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 8:02 AM, zheng l <zhengsfriend@hotmail.com> wrote:
Dear Dr. Meng
I used Chimera software for analyzing many protein crystal structures and then modified them and it has so faithfully doing job for me. However, this structure that I attached below is very difficult to modify.
The problem is that the hydrogens in structure are hidden. Usually when I need to, for example, replaces a carbon to a nitrogen in a Phe the nitrogen will attached with a hydrogen if I set to have 3 bond for the nitrogen. But this structure is not showing hydrogens at all
Would you please help me find a way of show all hydrogens need for modifying the protein structure?
Thank you!
Best regards!
Zhengzheng
<1tup chain b opt 2.pdb>