that's with the ISOSURFACE command? or by itself? You need
isosurface COLOR RANGE .
when creating the isosurface or, after the fact:
color ISOSURFACE range ...
if the isosurface is already created.
On Sat, Mar 12, 2011 at 2:05 PM, Eduardo Oliveira wrote:
> Hi Bob,
>
> I've tried COLOR
Hi Bob,
I've tried COLOR RANGE -0.025 0.025 but i got the same surface, with no
color change. I've tried color "colorSchemeName" RANGE [min] [max] too and
the same thing happened. What am i doing wrong?
--
Colocation vs. M
look for "range" in the online documentation
http://chemapps.stolaf.edu/jmol/docs/?search=color%20range#isosurfacecolorandcontouroptions
On Thu, Mar 10, 2011 at 10:35 PM, Eduardo Oliveira wrote:
> Hi Bob,
>
> Yeah i see that now, thanks. One last question, how can i change the color
> span to ab
Hi Bob,
Yeah i see that now, thanks. One last question, how can i change the color
span to absolute values? I wanted min and max values for the surface color
-0.025 and 0.025.
--
Colocation vs. Managed Hosting
A question a
You have to load the COSMO file, not the MOL file, both for the structure
and the surface. Do you have both the COSMO and the MOL files in some
directory? Just ignore the MOL files, I guess. You could use
Var data = load("?.cosmo")
if (data.find("java.io.FileNotFoundException")) { return }
Hi Bob,
Actually i didn't generate this .cos files, so i don't know if it was used
the .mol file and , therefore, i don't know if they were supposed to match.
But i think for my purpouse it would be easier to avoid creating a .jvxl
file, since i can use the function loadCosmo and it works. I would
So that makes sense to you that the COSMO and MOL files don't have the same
coordinates? Looks like one is rotated relative to the other.
On Wed, Mar 2, 2011 at 11:06 AM, Eduardo Oliveira wrote:
> Hi Bob,
>
> Yea i think you're right, kinda pointless generating a .jvxl file. I wanted
> to create
Hi Bob,
Yea i think you're right, kinda pointless generating a .jvxl file. I wanted
to create the jvxl file because i don't know how to enter that algorithm
without opening the console window. I wrote a little Java class and i wanted
it to open the .mol file along with the surface.
---
Ah, ok. That makes sense. The COSMO file itself must be reloaded, not the
mol file. I don't know where the COSMO file comes from, but it appears not
to have come from 1-chlorobutane.mol. (Or, if it did, then some program is
messing with that file! You need to load the COSMO file itself along with
t
By the way, with quaternions and the Jmol compare() function, we could write
a little function that would rotate the isosurface to match any mol file
coordinates.
Bob
On Fri, Feb 25, 2011 at 8:13 AM, Robert Hanson wrote:
> Ah, ok. That makes sense. The COSMO file itself must be reloaded, not th
Hi Bob,
I do the following steps:
1) I load 1-CHLOROBUTANE.mol
2) I open the console and enter this:
function loadCosmo(fname) {
print "reading " + fname
Var fdata = load(fname).split(" DATA")
Var atoms = fdata[2].lines[3][-2]
Var segments = fdata[3].lines[3][0]
Var n = atoms
nah! Are you sure you made those from the same coordinate file? Can you send
me some files? scripts that were used?
Bob
On Thu, Feb 24, 2011 at 12:03 PM, Eduardo Oliveira wrote:
> Hi Bob,
>
> I should've sent a picture to make my explanation clearer. That is what i
> get.
>
>
> -
Hi Bob,
I should've sent a picture to make my explanation clearer. That is what i get.
<>--
Free Software Download: Index, Search & Analyze Logs and other IT data in
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I'm certainly not seeing that. I do see that they don't have the rwb
colorscheme. So coming from the JVXL file you need to specify the color
scheme:
isosurface t2.jvxl colorscheme "rwb"*
*I realize that should not be necessary, but it is. The color scheme used is
not saved with the isosurface in
Hi Robert,
Sorry it took me so long to answer. Your algorithm worked just fine, thank
you!
However, i'm having another trouble now. After the surface is generated
everything is alright, i save it as a .jvxl file, then when i try to load it
to the same molecule, the surface and the molecule don't
(oh, by the way, that will require
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip, uploading
now...)
On Sat, Feb 19, 2011 at 7:31 PM, Robert Hanson wrote:
> Here you go!
>
> function loadCosmo(fname) {
> print "reading " + fname
> Var fdata = load(fname).split(" DATA")
>
Here you go!
function loadCosmo(fname) {
print "reading " + fname
Var fdata = load(fname).split(" DATA")
Var atoms = fdata[2].lines[3][-2]
Var segments = fdata[3].lines[3][0]
Var n = atoms.length + segments.length
fdata = "" + n + "\ndata are from " + fname + "\n"
print
OK, I see how to do this.
1) transform your data into what looks like an XYZ file, where the first
part is the actual atoms, and the second part is as set of "bogus" atoms
positioned where you need them and including the data you want to plot in
the fifth column. I made a little .xyz file using Ex
Hi Robert,
I think you got it. I just have some questions. Do these commands
given get the coordinates given by the file .cos? And do these
commands get the points from both sets of data ("atomic data" and
"segment data")? because i'm manly interested on segment data.
---
OK, so this is just a file that indicates partial charge, mostly. You could
write a little Jmol script that would map those charges onto a surface.
Something like the following:
Var fileData =
load("xxx.cos").split("SIGMA")[2].split("SEGMENT")[1].trim().lines
Var nLines = fileData.length
for (Va
Hi Robert,
I attached an example to this message. I would like to create a colored
surface in Jmol using x,y,z coordinates along with the SIGMA data. If there
is something unclear about the data, just ask me.
1-CHLOROBUTANE.cos
Description: Binary data
---
yes, please send an example.
On Thu, Feb 17, 2011 at 9:47 AM, Eduardo Oliveira wrote:
> Hi Robert,
>
> .cos files are files which contain data for (x,y,z) coordinates, that can
> generate a surface around the molecule. They are created by a program called
> MOPAC. If it helps, i could send an att
Hi Robert,
.cos files are files which contain data for (x,y,z) coordinates, that can
generate a surface around the molecule. They are created by a program called
MOPAC. If it helps, i could send an attachment with an example of a .cos
file.
-
what are .cos files? What program creates these?
On Thu, Feb 17, 2011 at 7:39 AM, Eduardo Oliveira wrote:
> Hi everyone,
>
> I have some surface data and i would like to generate a colored surface on
> Jmol, however the file format i'm using (.cos) is not supported by Jmol. I
> would like to know
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