[Chimera-users] Combine atom-spec non-alphanumeric no-nunderscore character error

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 30 13:03:22 PST 2019

Hi Ahmad,
The specification is wrong for two reasons:
(1) need colon instead of comma, for example #1:.k:.e
(2) you would need to either remove the space between the two models or put quotes around the whole thing like "#1:.k:.e #2:.k:.e"

However, more important is that “combine” will include all the atoms in the whole models even if you only specify some chains. It says this in the second paragraph:

So what you really wanted to do is to delete all the other atoms before you combine the two models, something like

select #1:.k:.e #2:.k:.e
delete ~sel
combine #1,2

(also make sure you really have models #1 and #2, since the first model is #0 and you might need to use #0 and #1 instead… check in the Model Panel, opened from Favorites menu)

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 30, 2019, at 11:23 AM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> I'm trying to combine a few chains from different models. I'm using: combine #1:.k,.e #2:.k,.e. I'm getting the above error, and I'm not sure why my selection isn't working! 
> Regards.  

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