[Chimera-users] Dynamic scolor custom cmap?

Fri Dec 13 13:15:33 PST 2013

Hi Tom,

This is perfect. I think this will work well for me. Thanks for the quick reply and the fix. Every time I think there might be a deficiency in Chimera, you all prove me wrong. And it is usually because you've already solved the problem before I ever thought there might be one!

Cheers,
Darrell 

Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

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----- Original Message -----
From: Tom Goddard [mailto:goddard at sonic.net]
Sent: Friday, December 13, 2013 04:10 PM
To: Hurt, Darrell (NIH/NIAID) [E]
Cc: Chimera-users at cgl.ucsf.edu List <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Dynamic scolor custom cmap?

Hi Darrell,

  There is a tricky undocumented feature that solves your problem.  If you specify the scolor option "cmapRange full" and you also specify the cmap option like "cmap 0,red:0.6,yellow:1,blue" or "cmap 0.2,green:0.8,yellow" then values from 0 to 1 in the cmap spec will be mapped linearly to the minimum to maximum full range values.  The documentation says the "full" is the default for the cmapRange option but that is not true.  Not using cmapRange simply does no range mapping on your specified cmap.

  I wrote this code and didn't adequately explain it to Elaine who wrote the documentation.  We will fix the documentation.

	Tom

On Dec 13, 2013, at 12:16 PM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh at niaid.nih.gov> wrote:

> Hi Chimera friends,
> 
> I have a volumetric potential file loaded that I want to map onto a molecular surface. For my application, I want the color mapping to use a custom palette of at least three colors that spans the full range of surface values.
> 
> I know that I can do this by simply specifying the custom colors in the Surface Color panel and then clicking "Set full range of surface values". That works for me.
> 
> However, I want to do this via command line. The following line works for me (I've omitted "cmapRange full" because that is the default setting):
> 
> scolor #0 volume #1 offset 1.4 cmap cyanmaroon
> 
> My problem become if I want to set a custom palette:
> 
> scolor #0 volume #1 offset 1.4 cmap -10,yellow:0,white:10,green
> 
> This line also works, but for values lower or higher than –10 or +10, the color ramp "plateaus". And this line only works because the extents of this particular mapping happen to go from –29 to +17.
> 
> Is it possible to obtain the values for the full range and specify them for a custom palette? Or is it possible to assign a custom palette and call it like the default palettes?
> 
> I'm happy to clarify if needed.
> 
> Thanks!
> Darrell
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Office: 301-402-0095
> Mobile: 301-758-3559
> Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
> Twitter: @niaidbioit<https://twitter.com/niaidbioit>
> 
> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> 
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