[Chimera-users] Matching of small molecules

Cassandra Ceccopieri cassandra.ceccopieri at hirszfeld.pl
Wed Nov 28 04:22:55 PST 2018

Dear Elaine,
thank you very much for your help.
Kind Regards,

----- Original Message -----
From: "Elaine Meng" <meng at cgl.ucsf.edu>
To: "Cassandra Ceccopieri" <cassandra.ceccopieri at hirszfeld.pl>
Cc: "chimera-users" <chimera-users at cgl.ucsf.edu>
Sent: Monday, 26 November, 2018 19:04:40
Subject: Re: [Chimera-users] Matching of small molecules

Hi Cassandra,
I don’t know what example you are viewing, but the word “at” is not used; it should be an at symbol @ without spaces before or after it:

match #0 at c5,c4,n7,c8,c9,s10  #1 at c9,c8,n11,c12,c13,s14

There’s a couple examples in the “hydrolases” tutorial. See also the “match” manpage, and general description of command-line atom specification:


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

> On Nov 23, 2018, at 1:24 AM, Cassandra Ceccopieri <cassandra.ceccopieri at hirszfeld.pl> wrote:
> Dear Sir/Madam,
> I would like to ask how to overcome the following problem that I faced trying to perform an alignment of small molecules. Writing in the command line section the following instruction:
> match #0 at c5,c4,n7,c8,c9,s10  #1 at c9,c8,n11,c12,c13,s14
> I obtain, as output, an error message saying: Error in "#0 at  c5,c4,n7,c8,c9,s10" must be an integer. 
> I checked the tutorial but the instruction for the command line seemed in the same format as mine. Therefore, I would like to ask assistance to be able to perform my analysis.
> Kind Regards,
> C.

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