OK, it's a consensus then -- those are the colors!
Frieda Reichsman wrote:
> I think these colors work well. Thanks for suggesting them, Angel.
> Frieda
>
> On Sep 23, 2006, at 2:39 PM, Angel Herraez wrote:
>
>> Glad you like them, Tim.
>> The reason for my proposal was that Jmol already uses man
right. nothing happens. It's just a calculation. Then use
select surfacedistance < 2.0; color red
for example. If you have solvent, it is best to use
select not solvent
calculate surface
select surfacedistanec < 2.0; color red
that sort of thing.
Angel Herraez wrote:
>On 15 Sep 2006 at 23:0
I have started documenting the different surfaces that can be rendered with
Jmol v11.
The basic part is done, although more needs to be written, and I am
planning a demo/testing page too.
http://biomodel.uah.es/pruebas/jmol/surface/inicio.htm
(also linked from my page in the Wiki)
Comments are
On 15 Sep 2006 at 23:06, Bob Hanson wrote:
[snip]
> also
>
> calculate surface
I cannot find how this works. The doc says
"Calculates the solvent-accessible surface"
but nothing happens.
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OK, I solved my "show pdbheader" problem easily enough.
The problem was not in the "show pdbheader" or messageCallback()
mechanisms, but rather in the workaround I used to send arbitrary messages
(to signal the beginning and end of the pdbheader message). I'm not sure
why that workaround no lon
I am attempting to test bug fixes I requested in 10.9.64, but have run into
two stumbling blocks.
1. "set picking on" (remains present in the script doc) generates an error,
invalid parameter. I send this to Jmol often in FirstGlance in Jmol. I am
guessing it is equivalent to "set picking ident
I think these colors work well. Thanks for suggesting them, Angel.FriedaOn Sep 23, 2006, at 2:39 PM, Angel Herraez wrote:Glad you like them, Tim.The reason for my proposal was that Jmol already uses many shades of blue, but not yellow, among element colors (http://jmol.sourceforge.net/jscolors/)I a
Timothy Driscoll wrote:
>On Sep 23, 2006, at 9:59 AM, Bob Hanson wrote:
>
>
>>>Jmol fails to connect some atoms with covalent bonds where there
>>>should be
>>>connections.
>>>
>>>
>>>
>>>
>>This is an intended feature, not a bug. In many PDB/mmCIF files, the
>>author has explicitly defi
Glad you like them, Tim.
The reason for my proposal was that Jmol already uses many shades of
blue, but not yellow, among element colors
(http://jmol.sourceforge.net/jscolors/)
I am not so sure they can be distinguished easily, but I think there is minor
trouble if all look like hydrogen, and t
On Sep 23, 2006, at 8:35 AM, Angel Herraez wrote:
> Hi
>
> After Eric's post on Jmol "lots of bugs", Bob has added support for
> deuterium and tritium --in fact, for any isotopes--. He has chosen
> to assign
> them helium and lithium colors.
> I have proposed on jmol-developers that unique color
On Sep 23, 2006, at 9:59 AM, Bob Hanson wrote:
>
>> Jmol fails to connect some atoms with covalent bonds where there
>> should be
>> connections.
>>
>>
> This is an intended feature, not a bug. In many PDB/mmCIF files, the
> author has explicitly defined quite a number of bond connections using
>
A few hours after 10.9.63, here's 10.9.64 available for download at
http://www.jmol.org/files/
Changes:
"If it contains main chain atoms, and it is
(1) ATOM or
(2) HETERO and bonded correctly,
call it protein or nucleic acid."
rather than
"If it contains main chain atoms, and it is bonded c
Just a follow up on this, since I haven't heard from Eric, and 11.0 is
just around the corner. This is a lengthy message.
Synopsis
1) Calcium as protein is fixed in 10.9.61.
2) The problem with situations where there are two groups in the same
chain with the same residue sequence numb
Thanks, Nico. The comment regarding save/restore selection is a bit
vague. Here's a better one:
save/restore selection
--
Jmol 10.9.63 allows saving and restoring of the current selection set
across file load boundaries. Note that this is slightly different from
"define" be
Hi everyone,
Jmol prerelease 10.9.63 is available for download at
http://www.jmol.org/files/
We want to release 11.0 in a near future, so test as much as you can so
we can fix bugs and deliver and really stable 11.0 :)
What needs to be done still before 11.0 :
- fixing a bug in the internationa
see http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm
Angel Herraez wrote:
>Bob, can you point us to a sample file for this?
>I can test it and compare with Chime, but I need a molecule to focus on.
>
>
>
Bob, can you point us to a sample file for this?
I can test it and compare with Chime, but I need a molecule to focus on.
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Hi Frieda,
Atoms show up similarly in both versions 103 and 10962 under Firefox
Windows.
I don't see any initial jump/reorientation in the second movie.
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