[Chimera-users] DNA superposition

Elaine Meng meng at cgl.ucsf.edu
Mon May 15 09:59:21 PDT 2017


Hi Marco,
Does that command do what you want?   To be safe, you should specify the atoms you want to use in the fit… maybe

match #0:.B #1:.B

(if the B chains have exactly the same atoms… otherwise you may need to specify residue number ranges, or P atoms only, or some other specification that is narrower than the whole chains.)

Elaine

> On May 15, 2017, at 9:47 AM, MarcoSette <sette at uniroma2.it> wrote:
> 
> 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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