[Chimera-users] DNA superposition

Elaine Meng meng at cgl.ucsf.edu
Mon May 15 10:06:36 PDT 2017


Hi Marco,
Another possibility is to use “matchmaker” instead of “match” and let it figure out the pairing if the DNA has the same or similar sequence, for example something like:

matchmaker #0:.B #1:.B pair ss matrix Nucleic show true

… where “show true” will show the sequence alignment used for the pairing.  See also the “iterate” option; some iteration will occur unless you specify “iterate false”

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

Elaine

> On May 15, 2017, at 9:59 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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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