Re: [Jmol-users] coloring surface residues

[Daniel Caffrey]

That works. Thank you!

On Fri, Jan 13, 2017 at 8:20 AM, Robert Hanson  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 
> 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 
>> wrote:
>>
>>> OK, I found it. An easy fix. will be in 14.8.1 to allowisosurface
>>> color "user" 
>>>
>>>
>>> On Thu, Jan 12, 2017 at 6:42 PM, Robert Hanson 
>>> 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 

Re: [Jmol-users] coloring surface residues

[Robert Hanson]

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 
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  wrote:
>
>> OK, I found it. An easy fix. will be in 14.8.1 to allowisosurface
>> color "user" 
>>
>>
>> On Thu, Jan 12, 2017 at 6:42 PM, Robert Hanson 
>> 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
> ___
> 

Re: [Jmol-users] coloring surface residues

[Daniel Caffrey]

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  wrote:

> OK, I found it. An easy fix. will be in 14.8.1 to allowisosurface
> color "user" 
>
>
> On Thu, Jan 12, 2017 at 6:42 PM, Robert Hanson  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___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] coloring surface residues

[Robert Hanson]

OK, I found it. An easy fix. will be in 14.8.1 to allowisosurface color
"user" 


On Thu, Jan 12, 2017 at 6:42 PM, Robert Hanson  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

Re: [Jmol-users] coloring surface residues

[Robert Hanson]

Q: Is the "ass" here just something that happened in the transmission by
email?

  ass255.0,255.0,0.0}

​
--
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