[Chimera-users] Questions regarding measuring distances between atoms

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 10 13:11:20 PDT 2020

Hi Yoel,
For (1) there must be some other step that causes problems, because after the following commands I still do not get any error messages.

open 5tby
~ribbon :.a,c,e

I can even delete those chains and still don't get any errors:

delete :.a,c,e

The kind of thing that might cause that "multiple chain IDs in chain" error is text-editing the PDB file manually (and making a mistake with chain IDs) or adding a bond between different chains.

> On Jul 10, 2020, at 8:07 AM, Sitbon, Yoel <yxs454 at miami.edu> wrote:
> Hi Elaine,
> Thank you for the message.
> For 1) I hide chain A, C and E for clarification purposes. That’s all.
> 2) it worked. Thank you
> Yoel.S
> -----Original Message-----
> From: Elaine Meng <meng at cgl.ucsf.edu> 
> Sent: Thursday, July 9, 2020 5:29 PM
> To: Sitbon, Yoel <yxs454 at miami.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Questions regarding measuring distances between atoms
> Hello Yoel,
> The error says there are multiple chain IDs in a chain.  I do not get this problem when I open 5tby directly from the RCSB PDB, so you must have changed the structure or edited the file in some way to cause it.  The way to avoid it is to not have multiple chain IDs for different atoms that are in the same chain, of course, but I can't say anything more detailed about how to fix it since I don't know how you got into that situation in the first place, sorry.
> For your second issue, I'm guessing you are trying to measure distances between sidechain atoms.  Only sidechain atoms are shown when ribbon is shown, since the ribbon prevents showing backbone atoms. Glycine is the one amino acid type that has no sidechain.  If you hide the ribbon you can show the backbone atoms and use some backbone atom of glycine for measuring distances.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Jul 9, 2020, at 12:25 PM, Sitbon, Yoel <yxs454 at miami.edu> wrote:
>> Hello,
>> My name is Yoel Sitbon and I am a Phd student at the University of Miami.
>> I started using chimera recently and I am running into a couple problems. Hopefully, you can help.
>> 	• I keep getting this error (please see picture attached). While it doesn’t interfere with what I am doing in terms of analysis, it does pop up every 5 seconds. Is there any way to fix it?
>> 	• I am using PDB file 5TBY, and I am trying to measure the distance between residues I788 in chain B and A57 in chain D. I am able to do that. However, when I mutate the residue 57 from Alanine to Glycine, the program cannot measure distances as it cannot locate atoms at 57. When I try to mutate to cysteine, it works.
>> Do you know why it is not allowing me to perform this?
>> Thank you for the help,
>> Yoel.S
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