[Chimera-users] DNA superposition

[Elaine Meng]

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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