Ops I missed it in the documentation, it works perfectly indeed. But I am
not able to specify the 0.0-8.0 range when mapping the property temperature
into an isosurface...
I made the following working code without specifying any range:
jmolScriptWait("frame none; isosurface SAS_3.1 select {3.1} sasurface 1.2
map property temperature colorscheme user; isosurface SAS_3.1 off;
isosurface SOLV_3.1 select {3.1} solvent 1.2 map property temperature
colorscheme user; isosurface SOLV_3.1 off; frame all;")
Then I hide/display with a checkbox. But how do I specify the 0.0-8.0 range?
I have tried the following possibilities without success:
map property temperature colorscheme user ABSOLUTE 0.0 8.0
map property temperature ABSOLUTE 0.0 8.0 colorscheme user
map property temperature colorscheme user; color isosurface property
temperature ABSOLUTE 0.0 8.0
map property temperature colorscheme user; color atoms property temperature
ABSOLUTE 0.0 8.0
map property temperature colorscheme user; color isosurface atoms property
temperature ABSOLUTE 0.0 8.0
Any idea? Thanks again!
Daniel
2011/4/1 Robert Hanson <hans...@stolaf.edu>
> sure
>
> color property temperature absolute 0.0 8.0
>
>
> On Fri, Apr 1, 2011 at 1:33 PM, Daniel Carbajo
> <daniel.carb...@gmail.com>wrote:
>
>> Thanks I know Jmol can calculate DSSP secondary structures, but I mainly
>> use it to calculate solvent accessibilities (secondary structures are a side
>> effect). I also use other programs like PSAIA or SPEEDFILL to calculate
>> other things... (my main concern it's not just show secondary structures,
>> solvent accessibilities or whatever on screen, but also provide the
>> transformed pdb text files for further studies). So I just used secondary
>> structures to illustrate the problem.
>> I will try "set rangeSelected" on Monday (I cannot do it during the
>> weekend), but what I need is not to specify a range of residues to color,
>> but a range of temperatures to consider (I know it's from 1 to 8 in the
>> secondary structure case, can't I just specify from 1 to 8, instead of
>> specifying the residues?)
>>
>> 2011/4/1 Robert Hanson <hans...@stolaf.edu>
>>
>>> Daniel,
>>>
>>> First note that Jmol has DSSP included now -- an authorized and verified
>>> implementation of "real" DSSP -- you should have no need to do this
>>> separately. I have no idea what you mean by "DSSP might crash" -- that's
>>> very odd. Why would DSSP crash? Anyway, if you just use
>>>
>>> calculate structure
>>>
>>> That gives you DSSP structure. These structure types include "helix310"
>>> "helixAlpha" "helixPi", "sheet", and "turn". The DSSP output also indicates
>>> isolated "bridge" residues, but although the hydrogen bonds are indicated
>>> using
>>>
>>> calculate hbonds structure
>>>
>>> we don't right now have a specific selection option for that. We also do
>>> not indicate "bend".
>>>
>>> But that really wasn't your question:
>>>
>>>
>>> On Fri, Apr 1, 2011 at 10:49 AM, Daniel Carbajo <
>>> daniel.carb...@gmail.com> wrote:
>>>
>>>>
>>>> It works properly until I load the homology models. They are all in blue
>>>> (the first color of the user color scheme). It seems like Jmol has taken
>>>> the
>>>> temperature range using the native structure temperature values. Since I
>>>> have loaded the native structure with the temperature values unchanged, the
>>>> range of these values do not go from 1 to 8, they go from 0 to around 100.
>>>> Then I load the homology models and they are all in blue since their
>>>> highest
>>>> value is 8 and falls in the first category if we count from 0 to around
>>>> 100....
>>>>
>>>>
>>> you need to
>>>
>>> set rangeSelected
>>>
>>> before you use
>>>
>>> color temperature
>>>
>>>
>>> That indicates that you want to set the color range based just on the
>>> selected residues.
>>>
>>> Bob
>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>>
>>>
>>> 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
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Create and publish websites with WebMatrix
>>> Use the most popular FREE web apps or write code yourself;
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>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Create and publish websites with WebMatrix
>> Use the most popular FREE web apps or write code yourself;
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>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
>
> ------------------------------------------------------------------------------
> Create and publish websites with WebMatrix
> Use the most popular FREE web apps or write code yourself;
> WebMatrix provides all the features you need to develop and
> publish your website. http://p.sf.net/sfu/ms-webmatrix-sf
>
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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