[Chimera-users] Rainbow command

Mark Rosenberg mark.rosenberg at manchester.ac.uk
Mon Aug 28 11:18:28 PDT 2017


Wonderful Tom and Elaine. I will try that too. Thank you so much.
> On 28 Aug 2017, at 18:06, Tom Goddard <goddard at sonic.net> wrote:
> 
> ChimeraX, our next generation of Chimera, is a bit nicer in that it can rainbow a single chain, for example “rainbow /b” to color just chain b.
> 
> 	Tom
> 
>> On Aug 28, 2017, at 9:57 AM, Mark Rosenberg  wrote:
>> 
>> Hi Elaine
>> That is wonderful. Thank you.
>> There is whole depth of logical information for me to follow.
>> Thank you so much.
>> Best
>> Mark
>>> On 28 Aug 2017, at 17:53, Elaine Meng  wrote:
>>> 
>>> Hi Mark,
>>> Short answer first and then a longer explanation.  The short answer is that “rainbow” always affects the whole model, i.e. you can’t just apply it to one chain in a model and not the others.  So the command is simply
>>> 
>>> rainbow
>>> 
>>> … or if you had more than one model, specifying the one you want, e.g.
>>> 
>>> rainbow #1
>>> 
>>> Longer explanation:
>>> I know it takes a little getting used to, but the “Usage” information on each command’s help page describes how to use the command.   ( Individual examples are helpful, but often fail to cover the specific thing each user wants to do.)
>>> 
>>> Usage notation:
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/usageconventions.html>
>>> 
>>> “rainbow” command help:
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html>
>>> 
>>> I’ was guessing you want to color the residues in a chain along the rainbow spectrum (one color per residue, not one color per chain).  That is the “residue” level, which is the default, so you don’t have to specify it.  If you want the standard rainbow colors starting with blue at N-term and ending with red at C-term, you don’t have to specify any colors either.  So the only thing you might want to specify is which atoms to apply the command to, the “atom-spec” in the usage.  In the usage, this links to a separate page because most commands have “atom-spec” and there are a lot of different ways to specify even the same set of atoms.
>>> 
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
>>> 
>>> However, as mentioned in the rainbow help page, it only affects the whole model.  For other commands that can apply to some specific chain, the atom-spec part could be something like
>>> 
>>> #0:.a   
>>> - model 0 chain A
>>> 
>>> :.c
>>> - all chains C in all models
>>> 
>>> … more examples here ...
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#subcats>
>>> 
>>> I hope this helps,
>>> Elaine
>>> ----------
>>> Elaine C. Meng, Ph.D. 
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>>> On Aug 28, 2017, at 4:51 AM, Mark Rosenberg  wrote:
>>>> 
>>>> Please can you provide an example of using Rainbow with Command line  for a specific chain so I can see how the nomenclature works. 
>>>> 
>>>> It would be so helpful if the Chimera help files could provide more examples like this so one can adapt them  to different situations.
>>>> 
>>>> Thank you.
>>> 
>> 
>> 
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> 




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