Matching of small molecules
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.
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@c5,c4,n7,c8,c9,s10 #1@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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/images.html#match...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> I hope this helps, Elaine ----- 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@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.
Dear Elaine, thank you very much for your help. Kind Regards, Cassandra ----- Original Message ----- From: "Elaine Meng" <meng@cgl.ucsf.edu> To: "Cassandra Ceccopieri" <cassandra.ceccopieri@hirszfeld.pl> Cc: "chimera-users" <chimera-users@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@c5,c4,n7,c8,c9,s10 #1@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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/images.html#match...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> I hope this helps, Elaine ----- 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@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.
participants (2)
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Cassandra Ceccopieri -
Elaine Meng