[Chimera-users] domain colouring

Elaine Meng meng at cgl.ucsf.edu
Tue May 27 14:52:29 PDT 2014


I'm afraid that is a larger philosophical discussion for some other forum (not a Chimera question for the chimera-users list).   I can only note that there are different definitions of domain, and different needs of researchers who are interested in them.  If you have solved the problem, maybe you can write a paper about it!

Elaine

On May 23, 2014, at 9:55 AM, ce <allderann at gmail.com> wrote:

> Hi E,
> 
> I am not familiar with the priorities of global biotechnology neverthelles taking into account benefits from protein folding and function prediction and classification it is unclear why automatic domains annotation is frighteningly delayed compared with the amount of sequenced data.
> 
> Is it realy so difficult to construct reliable domains positioning tool when strictly corelation between evolutionary order and the lack of random events is obvious ?  
> 
> 
> W dniu 2014-05-22 22:56, Elaine Meng pisze:
>> Hi J,
>> It is difficult to say what is the quickest way without more information about what you are doing.  As you may know, there are many different definitions of "domain" and different resources (database websites, web servers, publications, etc.) will say that the boundaries are in different places.   How to quickly show these on the 3D structure depends on which resource you are using and what kind of information they provide.  Further, I don't know if you are starting from only a structure or whether you have a sequence window already open.
>> 
>> I will try to answer, but it would help if you could be more specific with your future questions!
>> 
>> In general, you would go to the resource (SCOP website, or read the publication, etc.) and just look up the residue numbers for the start and end of the domain.  Then you can use the residue numbers in the command line of Chimera, e.g.:
>> 
>> color red,r :15.a-133.a
>> (color ribbon-only of residues 15-133 in chain A red)
>> 
>> If the website or other resource shows the domain on the sequence rather than as residue numbers, another way is to show the sequence of your structure in Chimera (main menu: Favorites… Sequence) and then on the sequence drag a box around the desired part, which will also select the corresponding part of the structure.  Then you can use the Actions menu to color the selected part, or command, e.g.: color red,r sel
>> 
>> If the domain is a feature annotation in UniProt, you can map that onto the sequence by using sequence-window menu item: "Info… UniProt Annotations" , then in the sequence window's Region Browser  click on the row for that annotation to show it on both the sequence with colored boxes and structure (if any) with selection.   Then you can use the Actions menu  or command to color the selected part, as above.  However, many UniProt entries don't have domain annotations.
>> 
>> I hope this helps,
>> 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 22, 2014, at 9:59 AM, ce 
>> <allderann at gmail.com>
>>  wrote:
>> 
>> 
>>> Hi,
>>> Could You send me instruction about domain colouring (the quickest way if possible) ?
>>> Cheers,
>>> J.
>>> 
> 
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