[Chimera-users] one more question

zheng l zhengsfriend at hotmail.com
Wed Nov 7 19:58:27 PST 2018

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!

From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, November 7, 2018 9:29 AM
To: zheng l
Cc: chimera-users
Subject: Re: 1up opt

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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