[Chimera-users] 1up opt

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 7 09:29:39 PST 2018

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:


(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

It is recommended to send questions to chimera-users at cgl.ucsf.edu (CC’ed here) in case I’m not available to answer.
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 at 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>

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