Rainbow by secondary structural element?
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.
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. 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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Oliver Clarke -
Tom Goddard