rainbow with atom-spec of a portion of a chain
I was trying to rainbow a subset of a chain using the rainbow command and the atom-spec: rainbow #0:34-102.a However when run, the entire chain A was colored with rainbow instead just residues 34-102 running the color command with the same atom-spec: color #FFFFFF #0:34-102.a produced the predicted result of only residues 34-102 being colored white Is there a command to rainbow only part of the chain or are there any workarounds to being able to rainbow only a selected portion of a chain? Thanks in advance Micah CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.
Hi Micah, Ah yes, you’ve run into a limitation mentioned in <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html> "The coloring cannot be limited to a subset of the polymer chains in a model or to a subset of the residues in a chain…” A somewhat laborious, inelegant workaround is to open two copies of the structure and from whichever one seems to “win” the display (can tell by model color), delete the non-rainbow portion and then rainbow that copy. However, due to the ribbon path interpolation, if you are showing ribbon the ends stick out from the full copy. You would need to further fudge things by including a 3-4 extra residues of overhang on both ends of the truncated copy and then undisplaying the ribbon for those overhangs. Then you don’t get the full rainbow range (the reddest and bluest parts are hidden) but it might be good enough for your purposes. Example: open 2gbp open 2gbp … still looks tan, so the first copy #0 is “winning” the display, delete from that one delete #0 & ~ :30-106 rainbow #0 ~ribb #0:30-33,103-106 modelcol white #1 … gives (at least for me) the appearance in the attached image. If you had the problem of the other model showing through, you could use Ribbon Style Editor to ensure that the ribbon of the rainbow copy is slightly fatter and wider than the other one. Sorry I didn’t have a nicer answer, but I hope this helps. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 13, 2017, at 10:34 AM, Cheng, Micah <Micah.Cheng@fccc.edu> wrote:
I was trying to rainbow a subset of a chain using the rainbow command and the atom-spec: rainbow #0:34-102.a
However when run, the entire chain A was colored with rainbow instead just residues 34-102 running the color command with the same atom-spec: color #FFFFFF #0:34-102.a produced the predicted result of only residues 34-102 being colored white Is there a command to rainbow only part of the chain or are there any workarounds to being able to rainbow only a selected portion of a chain?
Thanks in advance Micah
participants (2)
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Cheng, Micah -
Elaine Meng