[Chimera-users] Manually adjusting alignment

[Visvaldas K.]

Dear Elaine,
thank you for your reply! It does seem to work on my Mac. I have no idea why I had so many problems on Friday on my Linux workstation (chimera always kept complaining something about wrong domains... Perhaps I will try this again next week on Linux to see if it works there). Thank you and sorry for all the fuss!
Sincerely yours,
Vis@ Vilnius University


      From: Elaine Meng <meng at cgl.ucsf.edu>
 To: Visvaldas K. <coyote_v2002 at yahoo.com> 
Cc: "chimera-users at cgl.ucsf.edu Mailing List" <chimera-users at cgl.ucsf.edu>
 Sent: Friday, April 29, 2016 11:46 PM
 Subject: Re: [Chimera-users] Manually adjusting alignment
   
P.S. you don’t even need to look in the User’s Guide, you can show a table of the editing keys from the sequence window menu:  Edit… Show Editing Keys

Elaine

On Apr 29, 2016, at 8:11 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Vis Kairys,
> It sounds like the step you are missing is first making the stuff you want to move the “active region.”  You would do that by dragging a box around it with the mouse, or if you had already dragged a box but it was no longer active, clicking on it to make it active again (shown with dashed outline).  Then the various editing key combinations will move the residues in that box.
> 
> So the steps are:  drag box around the residues you want to move (the “RF”), Ctrl-left arrow to move it left
> 
> Multalign Viewer manpage:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
> … explanation of active region
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#activeregion>
> … editing keys
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#editing>
> 
> 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 Apr 29, 2016, at 2:07 AM, Visvaldas K. <coyote_v2002 at yahoo.com> wrote:
> 
>> Dear All,
>> 
>> I wasn't able to adjust alignment in the Alignment window, and search did not find an answer (because I get great number of false negatives)...
>> I tried shift-arrow, ctrl-shif-arrow and many times but only once the region moved "by accident", and I wasn't able to 
>> repeat this feat. 
>> 
>> To simplify the task, let's say I have in the alignment window:
>> 
>> seqA NQDF.RFRD
>> seqB MKTFIEHKD
>> 
>> I want to move "RF" by one residue to the left so that the top part becomes
>> 
>> NQDFRF.RD
>> 
>> What would be the sequence of keys, clicks/drags and so on to do that 
>> (also, how is the active region which is ready to move signified: green, green in a dashed frame, or perhaps white dashed frame)?
>> 
>> Sincerely yours,
>> 
>> Vis Kairys
>> 
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> 
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