[Chimera-users] DNA superposition

MarcoSette sette at uniroma2.it
Mon May 15 09:47:58 PDT 2017


Hi Elaine,

thanks for your help.
I would like to match only the DNA part of the complex (chain B in my 
case), and watch the different protein (chain A) orientation between the 
models.
If my command is
match #0 #1
I do not specify that the match should concern chains B.

Thanks again,
Marco


Il 15/05/2017 18.30, Elaine Meng ha scritto:
> 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


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