[Chimera-users] Alignment

[Eric Pettersen]

Hi Bodvael,
	Since it seems that numbering the strands in N->C order rather than  
SHEET record order would be an improvement, I am opening an  
enhancement-request in our bug-tracking database with you on the cc  
list so that you know when it gets implemented.  You should go ahead  
and use Elaine's suggestions since it will probably take awhile before  
it gets implemented.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Nov 15, 2011, at 4:44 PM, Elaine Meng wrote:

> Hi Bodvael,
> I don't understand the question.  Which numbering is the official  
> numbering?  Chimera has no way of knowing how a structure was  
> described in the manuscript about the structure.  It only knows what  
> is in the PDB file, and will number strands consecutively in the  
> order in which they are listed in the SHEET lines of the PDB file.   
> To tell what numbers Chimera assigned, use select commands  such as:
>
> select :/ssId=1 & strand
>
> You can manually reassign "ssId" to something different than what  
> Chimera assigned, using the command "setattr" -- for example, if you  
> want to change ssId of strand currently assigned as 2 to 3, command:
>
> setattr r ssId 3 strand&:/ssId=2
>
> ... but you would have to be very careful about the order in which  
> you do things.  The original strand 3 would still be 3 unless you  
> had changed it beforehand.  Also, does it ultimately matter which  
> numbers Chimera has assigned?  Not really, unless you are going to  
> use them for something. You could simply choose the strand you want  
> to act on by dragging in the sequence window, without using its  
> number.
>
> Numbering in terms of N->C, which may or may not be different from  
> what Chimera assigned using the order in the PDB file, can be  
> obtained by simply counting from N to C while viewing the structure  
> or sequence as described in my earlier message.
>
> 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 Nov 15, 2011, at 12:32 PM, bodvael email wrote:
>
>> Hi Elaine,
>>
>> Thanks a lot for your answer, it works.
>>
>> The reason I asked about the beta sheet numbers is because when I  
>> count the number regions highlighted in green from the N-term, my  
>> stretch of amino acids corresponds to beta sheet 7 instead of 5  
>> (based on the original manuscript).
>>
>> Thus, it appears that the numbering of the beta sheets in the  
>> linear sequence is different from their numbering in the ribbon  
>> diagram. My question is then, what is the best way to get the  
>> numbering of the secondary structure in the linear sequence but  
>> based on the "official" numbering in the ribbon diagram. Else it is  
>> a bit confusing to have different numbers for the same beta sheets.
>>
>> Thanks,
>> Bodvael
>>
>> On Tue, Nov 15, 2011 at 12:32 PM, Elaine Meng <meng at cgl.ucsf.edu>  
>> wrote:
>> Thanks Suda!
>>
>> Hi Bodvael,
>> I would only add:
>>
>> (A) To get strand number, it is probably best to do what Suda  
>> suggested:  if looking at the sequence, just count the strands  
>> (green boxes) from N to C, or if looking at the structure, follow  
>> the ribbon from N to C.  It may help to rainbow-color the  
>> structure, which by default goes from blue at the C-term to red at  
>> the N-term (Tools... Depiction... Rainbow in the menu, or command  
>> rainbow.
>>
>> Currently in Chimera the strand numbering is not necessarily from N- 
>> >C... they are numbered in order of appearance in the PDB SHEET  
>> records, and sometimes the order of the strands in a sheet is  
>> different from N->C order.  Keeping that in mind, you could select  
>> strands by number (will be shown with green highlighting on the  
>> structure) with commands, for example:
>>
>> select :/ssId=1 & strand
>>
>> (B) After you show the whole protein sequence as Suda said, you can  
>> search for some string of residues by choosing "Edit... Find  
>> Subsequence" from the sequence window menu.
>>
>> 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
>>
>>
>>
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