[Chimera-users] DNA superposition

Elaine Meng meng at cgl.ucsf.edu
Mon May 15 09:30:09 PDT 2017


Hi Marco,
A single “match” command only does a pairwise match… so if you wanted to match #1 to #0, #2 to #0, etc. it would need to be done in separate commands.  I believe your first example”match" command would superimpose #0-3 onto #4-7 (pairing #0 and #4, #1 and #5, etc.  Maybe it is hard to see that that is what happened.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>

The select commands are unnecessary.  The “match” command doesn’t care about the selection unless you use “sel” in the atom specification.

Assuming the models have tthe same atoms, your second “match” command example has an odd number of atoms ( models #5-7) and so it cannot do anything.

I hope this clarifies the situation,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On May 15, 2017, at 3:30 AM, Marco Sette <sette at uniroma2.it> wrote:
> 
> Hi all,
> 
> If I select multiple models of a protein-DNA complex
> select #0:1-40.B #1:1-40.B #2:1-40.B #3:1-40.B #4:1-40.B #5:1-40.B #6:1-40.B #7:1-40.B
> where B is the DNA and then match
> match #0 #1 #2 #3 #4 #5 #6 #7
> I obtain a message about the RMSD so it is working, but no superposition on the monitor...
> 
> Also, selection of part of the models
> select #5:1-40.B #6:1-40.B #7:1-40.B
> followed by
> match #5 #6 #7
> Report an error like
> "an even number of space-separated atom specs are required"
> Why? All atoms were selected. And in the previous case, where 8 models were selected using the same procedure, this message does not appear.
> 
> In both cases selection is done properly (as judged from the monitor) but the match command gives a not clear response.
> All DNA models have the same sequence. I miss something...
> I'm using version 1.11 of Chimera on Linux Ubuntu.
> 
> Thanks for your help,
> Marco




More information about the Chimera-users mailing list