Re: [Jmol-users] Creation / representation of aromatic bonds
That's a bug. It's showing up because your script uses set autobond false then proceeds to make the bonds. It's a bug only with NEW bonds. Fixed. Bob On Thu, Oct 2, 2008 at 6:03 PM, Dean Johnston <[EMAIL PROTECTED]> wrote: > > Have you tried 'calculate aromatic'? >> >> Regards, >> Rolf >> >> >> This message was sent using IMP, the Internet Messaging Program. >> >> > Yes, but in my case that produces alternating double bonds and dashed > single bonds - not a representation I've seen before. > > And I'm really looking for the proper set of connect commands that will > give a conventional aromatic representation (all six carbon-carbon bonds > with bond order 1.5, one solid bond and one dashed bond). > > Dean > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Creation / representation of aromatic bonds
> Have you tried 'calculate aromatic'? > > Regards, > Rolf > > > This message was sent using IMP, the Internet Messaging Program. > > Yes, but in my case that produces alternating double bonds and dashed single bonds - not a representation I've seen before. And I'm really looking for the proper set of connect commands that will give a conventional aromatic representation (all six carbon-carbon bonds with bond order 1.5, one solid bond and one dashed bond). Dean - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] problem reading spardir file
Hi Jeff, I have seen that sort of error when the Spartan file is open and you try and read it with Jmol. If you are using a Mac you can hold down option-alt while Exporting and select Jmol format for a multiple .xyz file. That is what i use. All the best Nick -- 3D Organic Animations http://www.chemtube3d.com Tel: +44 (0)151-794-3506 (3500 secretary) Message: 5 Date: Thu, 2 Oct 2008 16:13:42 -0400 From: Jeff Hansen <[EMAIL PROTECTED]> Subject: [Jmol-users] problem reading spardir file To: jmol-users@lists.sourceforge.net Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Could someone with experience using Spartan files in Jmol give me some help? What I did in Spartan is to create a butane molecule and save it. Then I defined a dihedral angle and did an Energy Profile calculation varying that dihedral angle from -180 to 180 with 24 steps. The results of that calculation were then saved separately. The first is called nbutane.spardir. The second is called butane.spardir. In Jmol the simpler nbutane.spardir file is displayed as expected. The second, butane.spardir, is not displayed and instead gives the following error message: Error reading file at line 7: BEGIN Directory Entry file:/Users/jeffhans/Sites/Jmol/jmol/models/ butane.spardir/M0001/proparc 9 for file file:/Users/jeffhans/Sites/Jmol/jmol/models/butane.spardir type spartan directory Does anyone know what I'm doing wrong and how to fix it so I can see this molecule in Jmol? What I'm looking to see is a file loaded that has multiple models so I can see each conformer. Thanks for any help you can provide. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** -- Message: 6 Date: Thu, 02 Oct 2008 23:26:23 +0200 From: [EMAIL PROTECTED] Subject: Re: [Jmol-users] Jmol 11.6 release -- delayed To: jmol-users@lists.sourceforge.net Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Quoting Robert Hanson <[EMAIL PROTECTED]>: Rolf, First, realize that it's an unusual situation that you are in, accessing files through an absolute path on your web server. Most of us use relative paths. This is not a bug. The problem is that that now that the signed applet can read from the hard drive, if you just say: /xxx/xxx/xxx Jmol has to assume that's from the hard drive, because it doesn't have a URL associated with it. (This was fixed recently for people on Macs and Unix boxes, where there is no X: prefix.) Whether or not the applet is signed doesn't make a difference -- we really don't want the signed and unsigned applet accessing different files. So you can no longer use load "/xxx/xxx" with no HTTP:// in front of it with the applet -- signed or unsigned -- to access root files on the web server. I suppose you could argue that we should allow "/" to mean "root on the web server" for the unsigned applet, but that would mean that the signed applet and unsigned applet would have two different interpretations, and I at least suggest that's not a good idea. Jmol now has to read that as a local file. Instead, use your full URL call, or set the default directory to http://[EMAIL PROTECTED]/ and then just use the load command without the initial slash. Will that work for you? Disabling server absolute paths is a severe change that at least should be announced very clearly. There might be other sites that will also be broken by this change. From the discussion about this topic on this list about 3 years ago (when the Jmol.js library popped up an alert when a server absolute path was used) I remember that there were also other people who voted for allowing server absolute paths. It is of course not always easy to maintain backward compatibility. But since the abilities of the signed applet are new features it might be better to disable server absolute paths by a switch instead of enabling them by a switch (or some other way) or disabling them totally. Q: What do others think about this? Q: Are there other Jmol sites that use server absolute paths? Regards, Rolf This message was sent using IMP, the Internet Messaging Program. -- Message: 7 Date: Thu, 2 Oct 2008 14:28:41 -0700 From: "Dean Johnston" <[EMAIL PROTECTED]> Subject: [Jmol-users] Creation / representation of aromatic bonds To: jmol-users@lists.sourceforge.net Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" I don't know if this is a bug or a feature, but my script to display a model of benzene ends up with all double bonds. Here is a snippet of the script (the struc
Re: [Jmol-users] Creation / representation of aromatic bonds
Quoting Dean Johnston <[EMAIL PROTECTED]>: > I don't know if this is a bug or a feature, but my script to display a model > of benzene ends up with all double bonds. Here is a snippet of the script > (the structure is defined via an inline data file): > > set autobond false; > data "model benzene" | ... (atom coordinates here) ... |end "model benzene"; > show data; > connect (atomno=1) (atomno=2) AROMATIC create; > connect (atomno=2) (atomno=3) AROMATIC create; > connect (atomno=3) (atomno=4) AROMATIC create; > connect (atomno=4) (atomno=5) AROMATIC create; > connect (atomno=5) (atomno=6) AROMATIC create; > connect (atomno=6) (atomno=1) AROMATIC create; > > This produces all double bonds. When I play around with the console, the > only way I can get what I want (and expect) is to say: > > connect; > connect (atomno=1) (atomno=2) AROMATIC modify; > ...etc. for all the remaining bonds > > I've attached a state file. > Have you tried 'calculate aromatic'? Regards, Rolf This message was sent using IMP, the Internet Messaging Program. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Creation / representation of aromatic bonds
I don't know if this is a bug or a feature, but my script to display a model
of benzene ends up with all double bonds. Here is a snippet of the script
(the structure is defined via an inline data file):
set autobond false;
data "model benzene" | ... (atom coordinates here) ... |end "model benzene";
show data;
connect (atomno=1) (atomno=2) AROMATIC create;
connect (atomno=2) (atomno=3) AROMATIC create;
connect (atomno=3) (atomno=4) AROMATIC create;
connect (atomno=4) (atomno=5) AROMATIC create;
connect (atomno=5) (atomno=6) AROMATIC create;
connect (atomno=6) (atomno=1) AROMATIC create;
This produces all double bonds. When I play around with the console, the
only way I can get what I want (and expect) is to say:
connect;
connect (atomno=1) (atomno=2) AROMATIC modify;
...etc. for all the remaining bonds
I've attached a state file.
Dean
# Jmol state version 11.6.RC17 2008-09-20 13:06;
# fullName = "jmolApplet0__18749094039234__";
# documentBase =
"http://dhj-macbook.local/~djohnston/symmetry/tutorial/benzene.html";;
# codeBase = "http://dhj-macbook.local/~djohnston/symmetry/common/Jmol/";;
function _setWindowState();
# height 591;
# width 591;
stateVersion = 1106000;
backgroundColor = "[xff]";
axis1Color = "[xff]";
axis2Color = "[x008000]";
axis3Color = "[xff]";
ambientPercent = 45;
diffusePercent = 84;
specular = true;
specularPercent = 22;
specularPower = 40;
specularExponent = 6;
statusReporting = true;
end function;
function _setFileState();
set allowEmbeddedScripts false;
set autoBond false;
set appendNew true;
set appletProxy "";
set applySymmetryToBonds false;
set bondRadiusMilliAngstroms 150;
set bondTolerance 0.45;
set defaultDirectory "";
set defaultLattice {0.0 0.0 0.0};
set defaultLoadScript "";
set defaultVDW Jmol;
set forceAutoBond false;
set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb";;
set minBondDistance 0.4;
set pdbSequential false;
set pdbGetHeader false;
set percentVdwAtom 20;
set smartAromatic true;
data "model inline"
12
benzene
C -1.2125 -0.70000.
C -1.21250.70000.
C0.1.40000.
C1.21240.70000.
C1.2124 -0.70000.
C0. -1.40000.
H -2.1478 -1.24000.
H -2.14781.24000.
H0.2.48000.
H2.14771.24000.
H2.1477 -1.24000.
H0. -2.48000.
end "model inline";;
end function;
function _setVariableState();
set defaultanglelabel "%VALUE %UNITS";
set defaultcolorscheme "Jmol";
set defaultdirectory "";
set defaultdistancelabel "%VALUE %UNITS";
set defaultdrawarrowscale 0.5;
set defaultlattice "{0 0 0}";
set defaultloadscript "";
set defaulttorsionlabel "%VALUE %UNITS";
set defaulttranslucent 0.5;
set defaultvdw "Jmol";
set allowembeddedscripts true;
set allowrotateselected false;
set appletproxy "";
set applysymmetrytobonds false;
set atompicking true;
set autobond false;
set autofps false;
set axes window;
set axesmode 0;
set axesscale 2.0;
set bondmodeor false;
set bondpicking false;
set bondradiusmilliangstroms 150;
set bondtolerance 0.45;
set cartoonrockets false;
set chaincasesensitive false;
set dataseparator "~~~";
set delaymaximumms 0;
set dipolescale 1.0;
set disablepopupmenu false;
set displaycellparameters true;
set dotdensity 3;
set dotsselectedonly false;
set dotsurface true;
set drawhover false;
set drawpicking false;
set dynamicmeasurements false;
set ellipsoidarcs false;
set ellipsoidaxes false;
set ellipsoidaxisdiameter 0.02;
set ellipsoidball true;
set ellipsoiddotcount 200;
set ellipsoiddots false;
set ellipsoidfill false;
set forceautobond false;
set greyscalerendering false;
set hbondsbackbone false;
set hbondssolid false;
set helppath "http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm";;
set hermitelevel 0;
set hidenameinpopup false;
set hidenavigationpoint false;
set highresolution false;
set historylevel 0;
set hoverdelay 0.5;
set isosurfacepropertysmoothing true;
set justifymeasurements false;
set loadformat "http://www.rcsb.org/pdb/files/%FILE.pdb";;
set measureallmodels false;
set measurementlabels true;
set messagestylechime false;
set minbonddistance 0.4;
set navigationperiodic false;
set navigationspeed 5.0;
set pdbgetheader false;
set pdbsequential false;
set percentvdwatom 20;
set pickingspinrate 10;
set picklabel "";
set pointgroupdistancetolerance 0.2;
set pointgrouplineartolerance 8.0;
set propertyatomnumbercolumncount 0;
set propertyatomnumberfield 0;
set propertycolorscheme "roygb";
set propertydatacolumncount 0;
set propertydatafield 0;
set quaternionframe "c";
set rangeselected false;
set ribbonaspectratio 16;
set ribbonborder false;
set rocketbarrels false;
set selectallmodels true;
set selecthetero
Re: [Jmol-users] Jmol 11.6 release -- delayed
Quoting Robert Hanson <[EMAIL PROTECTED]>: > Rolf, > > First, realize that it's an unusual situation that you are in, accessing > files through an absolute path on your web server. Most of us use relative > paths. > > This is not a bug. The problem is that that now that the signed applet can > read from the hard drive, if you just say: > > /xxx/xxx/xxx > > Jmol has to assume that's from the hard drive, because it doesn't have a URL > associated with it. (This was fixed recently for people on Macs and Unix > boxes, where there is no X: prefix.) > > Whether or not the applet is signed doesn't make a difference -- we really > don't want the signed and unsigned applet accessing different files. So you > can no longer use > > load "/xxx/xxx" > > with no HTTP:// in front of it with the applet -- signed or unsigned -- to > access root files on the web server. I suppose you could argue that we > should allow "/" to mean "root on the web server" for the unsigned applet, > but that would mean that the signed applet and unsigned applet would have > two different interpretations, and I at least suggest that's not a good > idea. > > Jmol now has to read that as a local file. Instead, use your full URL call, > or set the default directory to > > http://[EMAIL PROTECTED]/ > > and then just use the load command without the initial slash. > > Will that work for you? > Disabling server absolute paths is a severe change that at least should be announced very clearly. There might be other sites that will also be broken by this change. From the discussion about this topic on this list about 3 years ago (when the Jmol.js library popped up an alert when a server absolute path was used) I remember that there were also other people who voted for allowing server absolute paths. It is of course not always easy to maintain backward compatibility. But since the abilities of the signed applet are new features it might be better to disable server absolute paths by a switch instead of enabling them by a switch (or some other way) or disabling them totally. Q: What do others think about this? Q: Are there other Jmol sites that use server absolute paths? Regards, Rolf This message was sent using IMP, the Internet Messaging Program. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] problem reading spardir file
Could someone with experience using Spartan files in Jmol give me some help? What I did in Spartan is to create a butane molecule and save it. Then I defined a dihedral angle and did an Energy Profile calculation varying that dihedral angle from -180 to 180 with 24 steps. The results of that calculation were then saved separately. The first is called nbutane.spardir. The second is called butane.spardir. In Jmol the simpler nbutane.spardir file is displayed as expected. The second, butane.spardir, is not displayed and instead gives the following error message: Error reading file at line 7: BEGIN Directory Entry file:/Users/jeffhans/Sites/Jmol/jmol/models/ butane.spardir/M0001/proparc 9 for file file:/Users/jeffhans/Sites/Jmol/jmol/models/butane.spardir type spartan directory Does anyone know what I'm doing wrong and how to fix it so I can see this molecule in Jmol? What I'm looking to see is a file loaded that has multiple models so I can see each conformer. Thanks for any help you can provide. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 [EMAIL PROTECTED] *** - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 11.6 release -- delayed
Rolf,
First, realize that it's an unusual situation that you are in, accessing
files through an absolute path on your web server. Most of us use relative
paths.
This is not a bug. The problem is that that now that the signed applet can
read from the hard drive, if you just say:
/xxx/xxx/xxx
Jmol has to assume that's from the hard drive, because it doesn't have a URL
associated with it. (This was fixed recently for people on Macs and Unix
boxes, where there is no X: prefix.)
Whether or not the applet is signed doesn't make a difference -- we really
don't want the signed and unsigned applet accessing different files. So you
can no longer use
load "/xxx/xxx"
with no HTTP:// in front of it with the applet -- signed or unsigned -- to
access root files on the web server. I suppose you could argue that we
should allow "/" to mean "root on the web server" for the unsigned applet,
but that would mean that the signed applet and unsigned applet would have
two different interpretations, and I at least suggest that's not a good
idea.
Jmol now has to read that as a local file. Instead, use your full URL call,
or set the default directory to
http://[EMAIL PROTECTED]/
and then just use the load command without the initial slash.
Will that work for you?
Bob
On Thu, Oct 2, 2008 at 5:26 AM, Rolf Huehne <[EMAIL PROTECTED]> wrote:
> Robert Hanson wrote:
> > A few additional bugs were found just today; Nico has released 11.6.RC18
> --
> > those who found these bugs please check that they are fixed there, and we
> > will give it a few more days and release 11.6 this weekend.
> >
>
> 1) The problem with "vector_x = bound_box.x" is solved now.
>
> 2) 'getProperty("fileName")' now reports "zapped" after doing a 'zap'.
>
> 3) The "java.security.AccessControlException" problem still remains. I
> don't know if this is specific to our site because I can't check it
> with other sites. But it must be caused by changes introduced after
> 11.6.RC13 because the problem doesn't occur with this version or earlier
> ones.
> If I use the signed applet I get a "file not found" error instead.
> (Since the "file not found" error occurs before the
> "java.security.AccessControl" error I can't tell if the security problem
> doesn't occur there.)
>
> Regards,
> Rolf
>
> -
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ___
> 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
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
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Re: [Jmol-users] Jmol 11.6 release -- delayed
My problem with
{selected}.y = 0
has been solved too in RC18
-
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[Jmol-users] moving draw objects produces duplicates
I am with 11.6.RC18 doing something I've done before, but I am
finding a strange effect.
If it makes any sense, I will investigate further and report details.
1. I draw a small sphere using
draw pru diameter 0.3 {3.6 -1.35 1.4}
2. Then I activate
set picking draw
3. and move the object using Alt+drag. Instead of moving, the sphere
duplicates, that is, the original one stays there while I move the
new one.
4. If I request the info with
show draw
I get this:
draw ID "pru" diameter 0.3 [ 0 {3.6 -1.35 1.4} ] [ 1 {3.6 -1.35 1.4}
] [ 2 {3.6 -1.35 1.4} ] [ 3 {3.1282716 -1.4552727 1.9073887} ] ;
draw ID "pru" fill noMesh noDots notFrontOnly fullylit;
Is this intended, or meaningful, or just a byproduct or bug?
It was not happening with 11.5.x versions
-
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Re: [Jmol-users] Jmol 11.6 release -- delayed
Robert Hanson wrote:
> A few additional bugs were found just today; Nico has released 11.6.RC18 --
> those who found these bugs please check that they are fixed there, and we
> will give it a few more days and release 11.6 this weekend.
>
1) The problem with "vector_x = bound_box.x" is solved now.
2) 'getProperty("fileName")' now reports "zapped" after doing a 'zap'.
3) The "java.security.AccessControlException" problem still remains. I
don't know if this is specific to our site because I can't check it
with other sites. But it must be caused by changes introduced after
11.6.RC13 because the problem doesn't occur with this version or earlier
ones.
If I use the signed applet I get a "file not found" error instead.
(Since the "file not found" error occurs before the
"java.security.AccessControl" error I can't tell if the security problem
doesn't occur there.)
Regards,
Rolf
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
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