[Chimera-users] Rainbow by secondary structural element?

Tom Goddard goddard at sonic.net
Thu Jun 26 10:01:27 PDT 2014


On Jun 25, 2014, at 10:04 AM, Tom Goddard
Hi Oliver,

  I fixed “rainbow helix” so it uses a new rainbow for each chain — fixed in tonight’s daily build.  Also I added “rainbow strand” for coloring beta strands, and “rainbow sse” for coloring both helices and strands (secondary structure elements).

	Tom



Begin forwarded message:

> From: Oliver Clarke 
> Subject: Re: [Chimera-users] Rainbow by secondary structural element?
> Date: June 26, 2014 at 6:37:55 AM PDT
> To: Tom Goddard 
> 
> Hi Tom, I just tried out the “rainbow helix” command in the new daily build. I like it! 
> 
> Only one thing, it should operate independently within each chain I think, like for rainbow at the residue level - e.g. for an ion channel like 1BL8, helices in each chain should be colored consistently, rather than having a different color for each helix in the entire molecule - see attached snaps of 1bl8 monomer and tetramer to see what I mean - I think it should color each monomer consistently.
> 
> Thanks again for implementing this so fast!
> 
> Cheers,
> Oliver.
> 
> 
> On Jun 25, 2014, at 1:04 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
>> Hi Oliver,
>> 
>>   I added a “rainbow helix” command to Chimera, in tonight’s daily build.  Unfortunately it doesn’t look much different then simply using rainbow when applied to a transmembrane protein.  The two image below show "rainbow helix” and “rainbow” on 2rh1.
>> 
>> <2rh1_helices.jpg>      <2rh1_rainbow.jpg>
>> 
>> They are different since the rainbow helix command does not color the turns  and beta strands, and it has constant color on each helix, but those differences are hardly noticable.  I also discovered that the rainbow command only applies to whole models.  So it colors all helices even if you specify only the transmembrane residue range, so “rainbow helix :29-230,263-342” gives the same coloring as “rainbow helix”.
>> 
>> 	Tom
>> 
>> 
>> On Jun 25, 2014, at 8:01 AM, Oliver Clarke wrote:
>> 
>>> Hi all,
>>> 
>>> Currently, the rainbow function can operate at the levels of per residue, per chain or per model.
>>> 
>>> I was wondering whether it would be feasible in a future release to add an additional level, coloring per secondary structural element?
>>> 
>>> This would be particularly handy for structures of membrane proteins, where it is often desirable to color each helix/strand a different color, while not varying the color along the helix (and not coloring residues in loops etc). 
>>> 
>>> Even better would be to have separate “rainbow helix” “rainbow strand” and “rainbow secstruc” commands for finer control, but this is probably not really necessary.
>>> 
>>> Cheers,
>>> Oliver.
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
>> 
> 
 wrote:

> Hi Oliver,
> 
>   I added a “rainbow helix” command to Chimera, in tonight’s daily build.  Unfortunately it doesn’t look much different then simply using rainbow when applied to a transmembrane protein.  The two image below show "rainbow helix” and “rainbow” on 2rh1.
> 
> <2rh1_helices.jpg>      <2rh1_rainbow.jpg>
> 
> They are different since the rainbow helix command does not color the turns  and beta strands, and it has constant color on each helix, but those differences are hardly noticable.  I also discovered that the rainbow command only applies to whole models.  So it colors all helices even if you specify only the transmembrane residue range, so “rainbow helix :29-230,263-342” gives the same coloring as “rainbow helix”.
> 
> 	Tom
> 
> 
> On Jun 25, 2014, at 8:01 AM, Oliver Clarke wrote:
> 
>> Hi all,
>> 
>> Currently, the rainbow function can operate at the levels of per residue, per chain or per model.
>> 
>> I was wondering whether it would be feasible in a future release to add an additional level, coloring per secondary structural element?
>> 
>> This would be particularly handy for structures of membrane proteins, where it is often desirable to color each helix/strand a different color, while not varying the color along the helix (and not coloring residues in loops etc). 
>> 
>> Even better would be to have separate “rainbow helix” “rainbow strand” and “rainbow secstruc” commands for finer control, but this is probably not really necessary.
>> 
>> Cheers,
>> Oliver.
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 

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