OK, Dan, I found and fixed that one. The problem was that the command
*color isosurface range 1 122*
because it did not specify color scheme user:
*color isosurface "user" range 1 122*
reverted to the default color scheme, which is RGB.
I consider that a bug -- the scheme already specified for the isosurface
should always be used. So that is fixed, and also if you add "user" there,
it should work for you even without a Jmol update.
Bob
On Thu, Jan 12, 2017 at 7:22 PM, Daniel Caffrey <daniel.caff...@gmail.com>
wrote:
> Sorry there was a pasting issue (ass should have been { ) . I've pasted a
> better test case below where residues GLY3 and ARG9 should be colored pink.
>
> Replacing color with colorscheme takes care of the error - Thank you.
>
> Assuming I understand the expected behavior of the command, jmol is not
> assigning the specified colors to the correct residues. ARG9 is red instead
> of pink.
>
> load 3AB6.pdb
>
> set usercolorscheme {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,0,255.0}
> {255.0,127.5,0.0} {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,0,255.0} {255.0,127.5,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0}
> {255.0,127.5,0.0} {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,127.5,0.0}
> {255.0,127.5,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,127.5,0.0}
> {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,127.5,0.0} {255.0,127.5,0.0}
> {255.0,127.5,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0}
> {255.0,127.5,0.0} {255.0,127.5,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,127.5,0.0} {0.0,255.0,255.0} {0.0,255.0,255.0}
> {255.0,127.5,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,127.5,0.0}
> {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,127.5,0.0}
> {0.0,255.0,255.0} {0.0,255.0,255.0} {0.0,255.0,255.0} {0.0,255.0,255.0}
> {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,255.0,0.0} {0.0,255.0,255.0}
> {0.0,255.0,255.0} {0.0,255.0,255.0} {255.0,255.0,0.0} {255.0,127.5,0.0}
> {255.0,255.0,0.0} {0.0,255.0,255.0} {0.0,255.0,255.0} {0.0,255.0,255.0}
> {0.0,255.0,255.0} {255.0,127.5,0.0} {255.0,255.0,0.0} {255.0,127.5,0.0}
> {255.0,255.0,0.0} {255.0,255.0,0.0} {0.0,255.0,255.0} {0.0,255.0,255.0}
> {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,127.5,0.0}
> {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,255.0,0.0} {255.0,255.0,0.0}
> {255.0,255.0,0.0} {255.0,127.5,0.0} {255.0,127.5,0.0} {0.0,255.0,255.0}
> {255.0,127.5,0.0} {255.0,127.5,0.0} {0.0,255.0,255.0}
>
> isosurface select(*:A) ignore { ( hoh ) } molecular colorscheme 'user'
> map property resno; color isosurface range 1 122
>
>
>
> On Thu, Jan 12, 2017 at 7:51 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> OK, I found it. An easy fix. will be in 14.8.1 to allow isosurface
>> color "user" ....
>>
>>
>> On Thu, Jan 12, 2017 at 6:42 PM, Robert Hanson <hans...@stolaf.edu>
>> wrote:
>>
>>> The simple fix is to replace "color" with "colorscheme". I'm looking
>>> into why that is the case.
>>>
>>>
>>>
>>>
>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Developer Access Program for Intel Xeon Phi Processors
>> Access to Intel Xeon Phi processor-based developer platforms.
>> With one year of Intel Parallel Studio XE.
>> Training and support from Colfax.
>> Order your platform today. http://sdm.link/xeonphi
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
> ------------------------------------------------------------
> ------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today. http://sdm.link/xeonphi
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
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Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
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