Re: [Jmol-users] Set Picking Eror
Otis, from the top of my head, it used to be set picking none But maybe the others are/were also valid -- 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] Set Picking Eror
Thanks Angel. The top of your head works - so does set picking none. The document item at http://chemapps.stolaf.edu/jmol/docs/index.htm?fullmanual=1ver=12.2#setpicking should probably be edited. Actually, set picking off used to work, so maybe there is a bug. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org From: Angel Herráez angel.herr...@uah.es Sent: Thursday, February 24, 2011 11:08 AM To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] Set Picking Eror Otis, from the top of my head, it used to be set picking none But maybe the others are/were also valid -- 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 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] Set Picking Eror
sure enough -- set picking NONE # no problem set picking OFF# error -- invalid argument fixed for Jmol 12.0 and 12.1. see http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip Bob On Thu, Feb 24, 2011 at 9:50 AM, Otis Rothenberger osrot...@chemagic.comwrote: Bob, With 12.1.35, I'm getting the following error with both set picking off and set picking false: script ERROR: unrecognized SET PICKING SELECT parameter: false set picking false I've not noticed this before because as it turns out most of my set picking off commands do not matter! I finally noticed it with a situation where picking off is required. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org -- 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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