That works. Thank you!
On Fri, Jan 13, 2017 at 8:20 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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
>>> _______________________________________________
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>>> 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
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
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>>
>>
>
>
> --
> 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
>
>
------------------------------------------------------------------------------
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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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