Re: [Jmol-users] Help with surfaces
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. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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 eduardo...@gmail.comwrote: 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. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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 eduardo...@gmail.comwrote: 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 and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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 and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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 }
data = data.split( DATA)
to load that file with a dialog.
Bob
On Fri, Mar 4, 2011 at 5:19 AM, Eduardo Oliveira eduardo...@gmail.comwrote:
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 like to
know how to load those commands of the function without opening the console,
i want, once the .mol is loaded, the surface to open along with it, if it is
possible. I'm sending the Java class i created attached.
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Re: [Jmol-users] Help with surfaces
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 like to know how to load those commands of the function without opening the console, i want, once the .mol is loaded, the surface to open along with it, if it is possible. I'm sending the Java class i created attached. JmolTable.java Description: Binary data JmolLoadCompound.java Description: Binary data -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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 eduardo...@gmail.comwrote: 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. -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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. -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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 hans...@stolaf.edu wrote:
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
the JVXL file. Here's a revised function. Just call it as
loadCosmo(xxx.cos, false) before issuing the JVXL file. It's not clear to
me, if you have the COSMO file, why you would want to create a JVXL file.
Bob
function loadCosmo(fname, withSurface) {
if ( + withSurface == ) { withSurface = true } # default TRUE
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 nAtoms = + atoms.length + nSegments = + segments.length
for (Var i = 1; i =atoms.length; i++) {
Var radius = (atoms[i])[52][63]
fdata += (atoms[i])[6][51] + - + radius + \n
}
if (withSurface) {
for (Var i = 1; i =segments.length; i++) {
Var sigma = (segments[i])[77][88]
fdata += Xx + (segments[i])[17][52] + sigma + \n
}
load inline @fdata
isosurface select {not _XX} ignore {_XX} solvent 1.2 map select
{_XX} ignore {not _XX} property partialcharge colorscheme rwb
delete _Xx
} else {
load inline @fdata
}
}
On Thu, Feb 24, 2011 at 6:46 PM, Eduardo Oliveira eduardo...@gmail.comwrote:
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.length + segments.length
fdata = + n + \ndata are from + fname + \n
print nAtoms = + atoms.length + nSegments = + segments.length
for (Var i = 1; i =atoms.length; i++) {
Var radius = (atoms[i])[52][63]
fdata += (atoms[i])[6][51] + - + radius + \n
}
for (Var i = 1; i =segments.length; i++) {
Var sigma = (segments[i])[77][88]
fdata += Xx + (segments[i])[17][52] + sigma + \n
}
load inline @fdata
isosurface select {not _XX} ignore {_XX} solvent 1.2 map select
{_XX} ignore {not _XX} property partialcharge colorscheme rwb
delete _Xx
}
loadCosmo 1-CHLOROBUTANE.cos
3) I obtain picture nº 1
4) I right click FileSave jvxl surface
5) I obtain nº 2
6) I reload 1-CHLOROBUTANE.mol, open the console and write: isosurface
2.jvxl colorscheme rwb and i get nº3.
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St. Olaf College
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Northfield, MN 55057
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phone: 507-786-3107
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Re: [Jmol-users] Help with surfaces
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
the JVXL file. Here's a revised function. Just call it as
loadCosmo(xxx.cos, false) before issuing the JVXL file. It's not clear to
me, if you have the COSMO file, why you would want to create a JVXL file.
Bob
function loadCosmo(fname, withSurface) {
if ( + withSurface == ) { withSurface = true } # default TRUE
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 nAtoms = + atoms.length + nSegments = + segments.length
for (Var i = 1; i =atoms.length; i++) {
Var radius = (atoms[i])[52][63]
fdata += (atoms[i])[6][51] + - + radius + \n
}
if (withSurface) {
for (Var i = 1; i =segments.length; i++) {
Var sigma = (segments[i])[77][88]
fdata += Xx + (segments[i])[17][52] + sigma + \n
}
load inline @fdata
isosurface select {not _XX} ignore {_XX} solvent 1.2 map select
{_XX} ignore {not _XX} property partialcharge colorscheme rwb
delete _Xx
} else {
load inline @fdata
}
}
On Thu, Feb 24, 2011 at 6:46 PM, Eduardo Oliveira eduardo...@gmail.comwrote:
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.length + segments.length
fdata = + n + \ndata are from + fname + \n
print nAtoms = + atoms.length + nSegments = + segments.length
for (Var i = 1; i =atoms.length; i++) {
Var radius = (atoms[i])[52][63]
fdata += (atoms[i])[6][51] + - + radius + \n
}
for (Var i = 1; i =segments.length; i++) {
Var sigma = (segments[i])[77][88]
fdata += Xx + (segments[i])[17][52] + sigma + \n
}
load inline @fdata
isosurface select {not _XX} ignore {_XX} solvent 1.2 map select
{_XX} ignore {not _XX} property partialcharge colorscheme rwb
delete _Xx
}
loadCosmo 1-CHLOROBUTANE.cos
3) I obtain picture nº 1
4) I right click FileSave jvxl surface
5) I obtain nº 2
6) I reload 1-CHLOROBUTANE.mol, open the console and write: isosurface
2.jvxl colorscheme rwb and i get nº3.
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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
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Re: [Jmol-users] Help with surfaces
Hi Bob, I should've sent a picture to make my explanation clearer. That is what i get. attachment: 1-CHLOROBUTANE.jpg-- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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 eduardo...@gmail.comwrote: 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 Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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.length + segments.length
fdata = + n + \ndata are from + fname + \n
print nAtoms = + atoms.length + nSegments = + segments.length
for (Var i = 1; i =atoms.length; i++) {
Var radius = (atoms[i])[52][63]
fdata += (atoms[i])[6][51] + - + radius + \n
}
for (Var i = 1; i =segments.length; i++) {
Var sigma = (segments[i])[77][88]
fdata += Xx + (segments[i])[17][52] + sigma + \n
}
load inline @fdata
isosurface select {not _XX} ignore {_XX} solvent 1.2 map select
{_XX} ignore {not _XX} property partialcharge colorscheme rwb
delete _Xx
}
loadCosmo 1-CHLOROBUTANE.cos
3) I obtain picture nº 1
4) I right click FileSave jvxl surface
5) I obtain nº 2
6) I reload 1-CHLOROBUTANE.mol, open the console and write: isosurface
2.jvxl colorscheme rwb and i get nº3.
attachment: 1.jpg
1-CHLOROBUTANE.mol
Description: Binary data
attachment: 3.jpg
2.jvxl
Description: Binary data
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Re: [Jmol-users] Help with surfaces
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 match, it seems they have different coordinates. So i would like to know what i'm doing wrong. -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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 a JVXL file. You mean they are not matching? I'm certainly not seeing that. See attached images. Bob On Wed, Feb 23, 2011 at 5:08 PM, Eduardo Oliveira eduardo...@gmail.comwrote: 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 match, it seems they have different coordinates. So i would like to know what i'm doing wrong. -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 attachment: tcosmo.jpgattachment: tjvxl.jpg-- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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. -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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 Excel. But you could do it
with Jmol scripting as well. The file looks like this:
227
C -0.19 -0.309948 -0.463554
C 1.328281 -0.309948 -0.463554
C 1.829054 1.110428 -0.463554
C -0.729241 -1.734088 -0.479755
Cl 3.716621 0.988878 -0.443163
H -0.588478 0.23564 0.422575
H -0.588776 0.255435 -1.337048
H 1.723662 -0.86262 0.415297
H 1.724508 -0.861985 -1.342402
H 1.593678 1.690312 -1.36857
H 1.574928 1.697606 0.431649
H -1.828714 -1.759592 -0.479517
H -0.401381 -2.291613 -1.36905
H -0.400229 -2.311819 0.396145
Xx -1.033075 1.479272 -0.28151 -0.001523
Xx -2.098453 0.197779 -0.866198 0.000799
Xx -1.501445 1.182288 -0.589701 -0.001548
Xx -1.991341 0.484824 -0.769458 -0.000396
...
etc.
...
2) load that file.
3) set VDW radii.
4) create an isosurface for the atoms and color it by the partial charge
data in the segment data.
5) delete the unwanted atoms (segment positions).
Here's the script:
load t.xyz
{_H}.vdw = 1.416
{_C}.vdw = 2.006
{_Cl}.vdw = 2.365
isosurface select {not _XX} ignore {_XX} solvent 1.2 map select {_XX} ignore
{not _XX} property partialcharge colorscheme rwb
delete _XX
I think that's about as good as you can do. Could be interesting to
streamline this and allow mapping of any such point-based data. Have to
think about that
Bob
On Sat, Feb 19, 2011 at 5:31 PM, Robert Hanson hans...@stolaf.edu wrote:
These just use the coordinates from
load $1-chlorobutane
Presumably you have a model in some other file, right?
I see this in the file:
EPS=999.0 COSWRT RSOLV=1.2 RM1 NSPA=92
VDW(;H=1.416;C=2.006;N=1.829;O=1.7936;F=
1.7346;S=2.124;P=2.124;CL=2.365;BR=2.183;I=2.3364) GNORM=0.1 RELSCF=0.1
OK, I think I see part of what you are after, sort of. I plotted the points
in the SEGMENT section, and they appear to be points on a VDW surface. Jmol
can reproduce that surface using
load $1-chlorobutane
{_H}.vdw = 1.416
{_C}.vdw = 2.006
{_Cl}.vdw = 2.365
isosurface solvent 1.2
and every point is on it. Note, by the way, that this is NOT a
solvent-accessible surface; it's a solvent-excluded surface.
Q: Is that what you expected -- solvent-excluded, not solvent-accessible?
Q: These are rather unusual Van der Waals radii. Where do they come from?
Jmol by default uses H=1.1, C = 1.7, Cl 1.75. Why are these VDW radii so
large?
Q: How does a segment have only a point (and not, perhaps, three points)
and still have an area?
Q: I see the COSMO-CHARGE column is basically all zeros. What is the
significance of the SIGMA column?
I don't have access to Perkin Transactions, so I need your help
understanding the purpose of these values.
But, basically, I think what you want to do is create a surface that is
based on values at those points. What we need are triangles, not points.
Nothing here gives any clue as to how to connect those dots into triangles?
Jmol doesn't do that by itself. I suppose we could write something that does
that, but
--
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
attachment: t.jpg--
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Re: [Jmol-users] Help with surfaces
(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 hans...@stolaf.edu wrote:
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 nAtoms = + atoms.length + nSegments = + segments.length
for (Var i = 1; i =atoms.length; i++) {
Var radius = (atoms[i])[52][63]
fdata += (atoms[i])[6][51] + - + radius + \n
}
for (Var i = 1; i =segments.length; i++) {
Var sigma = (segments[i])[77][88]
fdata += Xx + (segments[i])[17][52] + sigma + \n
}
load inline @fdata
isosurface select {not _XX} ignore {_XX} solvent 1.2 map select {_XX}
ignore {not _XX} property partialcharge colorscheme rwb
delete _Xx
}
loadCosmo xxx.cos
--
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
--
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
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Re: [Jmol-users] Help with surfaces
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 (Var i = 1; i = nLines; i++) {
{atomno=i}.property_sigma = 0.0 + (fileData[i])[88][0]
}
isosurface molecular map property_sigma translucent
Is that the idea?
Bob
On Thu, Feb 17, 2011 at 6:52 PM, Eduardo Oliveira eduardo...@gmail.comwrote:
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.
--
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
___
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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
--
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb___
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Re: [Jmol-users] Help with surfaces
what are .cos files? What program creates these? On Thu, Feb 17, 2011 at 7:39 AM, Eduardo Oliveira eduardo...@gmail.comwrote: 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 more about the structure of .jvxl files, in order to convert these files. Thanks for your help. -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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. -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
yes, please send an example. On Thu, Feb 17, 2011 at 9:47 AM, Eduardo Oliveira eduardo...@gmail.comwrote: 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. -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help with surfaces
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 -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
