Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
Same for me with Mac Mail. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jun 1, 2010, at 10:10 PM, rgb wrote: > Otis Rothenberger wrote: >> Bob, >> >> This is the cat's meow. Thanks for the help. I'm still stuck with a >> server side approach (AJAX very frustrating!), but the "Jmol load >> completed" approach seems to work. Cholestane is below. What a slick >> way to communicate 3D models via email: >> >> http://chemagic.com/web_molecules/script_page_large.aspx?smiles=...@h]%28%28c%29c%29[c@H]1CC[C@@H]2[C@@]1%28c...@h]3[c@H]2CCC4[C@@]3%284%29C%29C >> >> For the JME applet on our page, I'm now using a choice of two load >> links - jmeFile or smiles. >> >> I'm interested in how the above link works on Mac. Also, note that the >> jmol javascript command does not work with Windows MSIE 8, so the >> above link does not work on MSIE. On this problem, MSIE ignores the >> following from the console: > In thunderbird 2.0 (on a mac) the link isn't recognised as one (stops at > the first [ character) but if I copy the whole thing and paste it into > FF 3.6 (or safari 4.0) it works just fine. > > You do appear to have misspelled your last name on the page though. :-) > > Rich > > > -- > > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
Otis Rothenberger wrote: > Bob, > > This is the cat's meow. Thanks for the help. I'm still stuck with a > server side approach (AJAX very frustrating!), but the "Jmol load > completed" approach seems to work. Cholestane is below. What a slick > way to communicate 3D models via email: > > http://chemagic.com/web_molecules/script_page_large.aspx?smiles=...@h]%28%28c%29c%29[c@H]1CC[C@@H]2[C@@]1%28c...@h]3[c@H]2CCC4[C@@]3%284%29C%29C > > For the JME applet on our page, I'm now using a choice of two load > links - jmeFile or smiles. > > I'm interested in how the above link works on Mac. Also, note that the > jmol javascript command does not work with Windows MSIE 8, so the > above link does not work on MSIE. On this problem, MSIE ignores the > following from the console: In thunderbird 2.0 (on a mac) the link isn't recognised as one (stops at the first [ character) but if I copy the whole thing and paste it into FF 3.6 (or safari 4.0) it works just fine. You do appear to have misspelled your last name on the page though. :-) Rich -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] JMol javascript thinks http address is local ....
Hi guys : The following code snippet is attempting to display a pdb file in
jmol, by getting it from the http location .
However, it bugs out on me, complaining that the file is not found at
'localhost:/http://www.rcsb.org/pdb/files/1I78.pdb1.gz'
jmolInitialize("jmol/",true);
jmolSetCallback("loadStructCallback","myStructCallback");
jmolSetCallback("messageCallback", "myMessageCallback");
jmolSetCallback("pickCallback", "myPickCallback");
jmolApplet(["100%","100%"], "load 'http://www.rcsb.org/pdb/files/1I78.pdb1.gz');
This is strange, it seems as though jmol doesnt realize im trying to load
via http ? It thinks the path is local to the pdb file.
Any ideas ?
--
Jay Vyas
MMSB/UCHC
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Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
Bob,
This is the cat's meow. Thanks for the help. I'm still stuck with a
server side approach (AJAX very frustrating!), but the "Jmol load
completed" approach seems to work. Cholestane is below. What a slick way
to communicate 3D models via email:
http://chemagic.com/web_molecules/script_page_large.aspx?smiles=...@h]%28%28c%29c%29[c@H]1CC[C@@H]2[C@@]1%28c...@h]3[c@H]2CCC4[C@@]3%284%29C%29C
For the JME applet on our page, I'm now using a choice of two load links
- jmeFile or smiles.
I'm interested in how the above link works on Mac. Also, note that the
jmol javascript command does not work with Windows MSIE 8, so the above
link does not work on MSIE. On this problem, MSIE ignores the following
from the console:
javascript alert("rats")
The message returned is:
evalintermediatevaluetoreturn = eval >> ( << "!!_jmol.noEval" )
Chrome and Firefox work just fine - link load and simple alert.
Unfortunately, MSIE never sees the Jmol loaded function.
I think the stereochemisrty of cholestane transferred correctly.
Otis
On 6/1/2010 12:37 PM, Robert Hanson wrote:
On Tue, Jun 1, 2010 at 9:03 AM, Otis Rothenberger
mailto:osrot...@chemagic.com>> wrote:
Bob,
You may have told me before, but I forget. How do you signal
JavaScript that the Jmol applet is loaded? I've tried putting a
Jmol javascript command into the Jmol load script, but MSIE seems
to ignore this.
jmolApplet(300, "load ;javascript 'loadDone()' ")
Sorry -- my error -- in this case you need double quotes or no quotes,
not single quotes (because it is in the class of commands such as echo
and message. That should read:
jmolApplet(300, 'load ;javascript "loadDone()" ')
AJAX would be nice, but I can't get past the cross domain security
issue with the unsigned applet. The signed applet scares many
users, so I'm using my server to get past this issue.
Unfortunately, this means each SMILES to mofile is a new load on
my page.
AJAX would be perfect. Just have the applet issue the above loadDone()
function, and then have the AJAX just return the data as text from IU
to a JavaScript function. I know, it's tricky to do this right with
different browsers
Getting the returned molfile into into a JavaSript variable is a
bit convoluted with ASP.NET , but it's doable.
Normally this is not a problem, but the line feeds create a
problem in the case of the molfile. I have to go to a hidden field
and then transfer to a JavaScript variable.
Sounds retro.
Anyway, with the above stage set, I just need to be able to hold
the JavaScript load to Jmol off until the applet is loaded.
right - switch those quotes.
Otis
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Re: [Jmol-users] translation change
My opinion: 1. I agree that we must stress the recommendation to use the split applet files. I'll take a look at the Wiki page to reinforce this. 2. I don't agree about removing the translations from the monolithic applet. If someone decides to use it for some reason (e.g. for local testing without having to drag around the whole bunch of files, as I did once recently), the translation would be desirable. And having a big applet is perhaps the strongest reason to convince people to stop using it and favor the split version! -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] translation change
I made a change in the most recent development version of Jmol, but before we consider it for Jmol 12.0, I'd like input: Problem: JmolApplet.jar and JmolAppletSigned.jar are getting VERY large (2 Mb) Problem: approximately 30% of the size of the applet is translations. Comment: It seems unnecessary to deliver to the user all translations for all languages whenever the "full applet" is loaded. Also, we really want to discourage use of the full applet files, since they will unnecessarily slow down applet loading. Solution: Include translations only in the fast-loading versions of Jmol -- JmolApplet0.jar and JmolAppletSigned0.jar -- and make it clearer that these are the preferred files by moving the those two entries at http://wiki.jmol.org/index.php/Files_Description down to the bottom. Comments? Bob -- 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] set defaults pymol (Robert Hanson)
Wayne, would you like to suggest a set of defaults that would work? Maybe in consultation with your colleagues at U Mass? Bob On Tue, Jun 1, 2010 at 1:45 PM, Wayne Decatur wrote: > Hi Bob, > Anything that lowers the hurdle to bringing users view high quality visuals > when they need them is a good thing. A general command such as this would be > nice. > Wayne > > In response to: > "Would it be reasonable to have a setting "set defaults Pymol" that matches > settings in Pymol\? For example, perhaps something that would make the > cartoons come up virtually identically to the way they appear in Pymol, and > have antialiasDisplay on? > > Bob" > > > > -- > > > ___ > 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] set defaults pymol (Robert Hanson)
Hi Bob, Anything that lowers the hurdle to bringing users view high quality visuals when they need them is a good thing. A general command such as this would be nice. Wayne In response to: "Would it be reasonable to have a setting "set defaults Pymol" that matches settings in Pymol\? For example, perhaps something that would make the cartoons come up virtually identically to the way they appear in Pymol, and have antialiasDisplay on? Bob" -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
On Tue, Jun 1, 2010 at 9:03 AM, Otis Rothenberger wrote: > Bob, > > You may have told me before, but I forget. How do you signal JavaScript > that the Jmol applet is loaded? I've tried putting a Jmol javascript command > into the Jmol load script, but MSIE seems to ignore this. > > jmolApplet(300, "load ;javascript 'loadDone()' ") Sorry -- my error -- in this case you need double quotes or no quotes, not single quotes (because it is in the class of commands such as echo and message. That should read: jmolApplet(300, 'load ;javascript "loadDone()" ') > AJAX would be nice, but I can't get past the cross domain security issue > with the unsigned applet. The signed applet scares many users, so I'm using > my server to get past this issue. Unfortunately, this means each SMILES to > mofile is a new load on my page. > AJAX would be perfect. Just have the applet issue the above loadDone() function, and then have the AJAX just return the data as text from IU to a JavaScript function. I know, it's tricky to do this right with different browsers > > Getting the returned molfile into into a JavaSript variable is a bit > convoluted with ASP.NET, but it's doable. Normally this is not a problem, > but the line feeds create a problem in the case of the molfile. I have to go > to a hidden field and then transfer to a JavaScript variable. > Sounds retro. > > Anyway, with the above stage set, I just need to be able to hold the > JavaScript load to Jmol off until the applet is loaded. > right - switch those quotes. > > Otis > > > > > > On 6/1/2010 9:24 AM, Robert Hanson wrote: > > tisk tisk! Never use setTimeout to do the Jmol load. Use a call FROM Jmol > indicating it has loaded to trigger your AJAX call or whatever. > > On Mon, May 31, 2010 at 6:02 PM, Otis Rothenberger > wrote: > >> Bob, >> >> Right now I pass it from a server variable to a hidden field on the page >> load. This is followed by an onLoad call to a TimeOut() load into Jmol. I >> suspect that timing is the issue. I have to find a better way to do it. AJAX >> per your subsequent email may be the answer. If I understand AJAX, I will >> not have to do a new page load. >> >> I'm also having problems with triple bonds (#) in the query string. I >> guess I need to try sending escaped text. >> >> Otis >> >> > -- > Otis Rothenbergerchemagic.com > > > > -- > > > ___ > 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
Bob, You may have told me before, but I forget. How do you signal JavaScript that the Jmol applet is loaded? I've tried putting a Jmol javascript command into the Jmol load script, but MSIE seems to ignore this. AJAX would be nice, but I can't get past the cross domain security issue with the unsigned applet. The signed applet scares many users, so I'm using my server to get past this issue. Unfortunately, this means each SMILES to mofile is a new load on my page. Getting the returned molfile into into a JavaSript variable is a bit convoluted with ASP.NET, but it's doable. Normally this is not a problem, but the line feeds create a problem in the case of the molfile. I have to go to a hidden field and then transfer to a JavaScript variable. Anyway, with the above stage set, I just need to be able to hold the JavaScript load to Jmol off until the applet is loaded. Otis On 6/1/2010 9:24 AM, Robert Hanson wrote: tisk tisk! Never use setTimeout to do the Jmol load. Use a call FROM Jmol indicating it has loaded to trigger your AJAX call or whatever. On Mon, May 31, 2010 at 6:02 PM, Otis Rothenberger mailto:osrot...@chemagic.com>> wrote: Bob, Right now I pass it from a server variable to a hidden field on the page load. This is followed by an onLoad call to a TimeOut() load into Jmol. I suspect that timing is the issue. I have to find a better way to do it. AJAX per your subsequent email may be the answer. If I understand AJAX, I will not have to do a new page load. I'm also having problems with triple bonds (#) in the query string. I guess I need to try sending escaped text. Otis -- Otis Rothenberger chemagic.com -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] surface representations of atom selections
Sure. That's better than geosurface. Geosurface should only be used with full molecules, not partial surfaces, as it's rather ragged on the "inside". On Tue, Jun 1, 2010 at 8:53 AM, Roni Gordon wrote: > At 2010-06-01 09:24, you wrote: > >From: Robert Hanson > >Subject: Re: [Jmol-users] surface representations of atom selections > > > >Check the documentation regarding the isosurface command and the > >options SELECT and IGNORE. Some combination of those two will do > >exactly what you want. If you use SASURFACE and you want the same > >scale as geosurface or dots or spacefill, be sure to use SASURFACE 0. > > > >Some reason not to just use spacefill? Or are you already using that > >within a translucent surface? > > > >I should probably remove the geosurface-dots motion business. It's > >not a much-used shape, and I'm not sure it makes any real difference > >in rendering speed. > > > >Bob > > I didn't realize that IGNORE did more than just invert the SELECT > expression -- I'll give it a shot. And the reason I'm using the > isosurface is for the mesh effect. > > Roni > > > > -- > > ___ > 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] surface representations of atom selections
At 2010-06-01 09:24, you wrote: >From: Robert Hanson >Subject: Re: [Jmol-users] surface representations of atom selections > >Check the documentation regarding the isosurface command and the >options SELECT and IGNORE. Some combination of those two will do >exactly what you want. If you use SASURFACE and you want the same >scale as geosurface or dots or spacefill, be sure to use SASURFACE 0. > >Some reason not to just use spacefill? Or are you already using that >within a translucent surface? > >I should probably remove the geosurface-dots motion business. It's >not a much-used shape, and I'm not sure it makes any real difference >in rendering speed. > >Bob I didn't realize that IGNORE did more than just invert the SELECT expression -- I'll give it a shot. And the reason I'm using the isosurface is for the mesh effect. Roni -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] News flash: Jmol reads SMILES into 3D format.
Jmol 12.0.RC16 adds full support for SMARTS "bond logic":
select smarts("A-,=;@A")
"select all bonded non-aromatic atoms (AA)
that are connected by single or double bonds (-,=)
in rings(;@)"
I believe I have a well-articulated schema for Jmol 3D-SMARTS. This can be
found at
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/smiles/package.html#specs
Is this the one and only such specification?
Bob
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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
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Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model
tisk tisk! Never use setTimeout to do the Jmol load. Use a call FROM Jmol indicating it has loaded to trigger your AJAX call or whatever. On Mon, May 31, 2010 at 6:02 PM, Otis Rothenberger wrote: > Bob, > > Right now I pass it from a server variable to a hidden field on the page > load. This is followed by an onLoad call to a TimeOut() load into Jmol. I > suspect that timing is the issue. I have to find a better way to do it. AJAX > per your subsequent email may be the answer. If I understand AJAX, I will > not have to do a new page load. > > I'm also having problems with triple bonds (#) in the query string. I guess > I need to try sending escaped text. > > Otis > > > On 5/31/2010 6:33 PM, Robert Hanson wrote: > > Otis, I had to load that page twice to have it work. Don't know why... > > Bob > > On Mon, May 31, 2010 at 1:09 PM, Otis Rothenberger > wrote: > >> Hello Miguel, >> >> I have Bob's IU server page discovery hooked to an unsigned applet via >> our server at chemagic. The following link should take you directly to >> the model your son needs: >> >> http://chemagic.com/web_molecules/script_page_large.aspx?smiles=C=CCSO >> >> >> Otis >> >> >> >> >> On 5/31/2010 2:01 PM, Angel Herráez wrote: >> > Coolest method: >> > >> > 1. find the SMILES string for 2-propenyl sulfenic acid >> > 2. get the latest Jmol 12.0.RC >> > 3. open the script console >> > 4. type >> > load "$C=CCSO" >> > 5. watch the 3D structure appear in Jmol >> > >> > Kudos to Bob! >> > >> > >> > >> > >> -- >> > >> > ___ >> > Jmol-users mailing list >> > Jmol-users@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/jmol-users >> > >> > >> >> -- >> Otis Rothenberger >> chemagic.com >> >> >> >> >> >> -- >> >> ___ >> 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 > > > -- > > > > > ___ > Jmol-users mailing > listjmol-us...@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users > > > -- > Otis Rothenbergerchemagic.com > > > > -- > > > ___ > 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] SMILES
It's a cludgy interface. You need to escape all the characters EXCEPT forward slash "/". I'll suggest they fix that. Hard to believe they did this without a "?" after SMILES, but that's what they did. On Mon, May 31, 2010 at 8:14 PM, Otis Rothenberger wrote: > Bob, > > Do you have any idea why this is returning propane and not 1-butyne? > > http://cheminfo.informatics.indiana.edu/rest/thread/d3.py/SMILES/CCC#C > > Otis > > > > On 5/31/2010 6:37 PM, Robert Hanson wrote: > > You could get it into a JavaScript variable using AJAX and then do anything > you want with it. > > Bob > > > On Sun, May 30, 2010 at 9:03 AM, Otis Rothenberger > wrote: > >> Bob, >> >> Following your note on SMILES (very nice addition by the way), I've been >> playing around with the Indiana University site. Since I have sever side >> programming control, I had no problem reading the IU http into a hidden >> field with subsequent load into the unsigned Jmol applet. I have to do >> this (the load) with JavaScript, however, and I was wondering about a >> direct load to Jmol. The IU return string (molfile) uses line-feeds. >> Below is their return for propane with bars replacing line-feeds. Is >> there any way to doctor this string so that Jmol will read it on a new >> load? I could write the unaltered file it to a temp file on the server >> and then load that as a molfile, but I'm curious about the possibility >> of reading the http stream into Jmol from my server directly on a fresh >> load. >> >> The UI file for propane with aforementioned line-feed swap: >> >> | PCMODEL v9.1 1.0 0.0|| 11 10 0 0 0 0 1 V2000| 1.3793 0.6283 >> 0.5851 C 0 0 0 0 0 0 | 2.1939 1.8713 0.9005 C 0 0 0 0 0 0 | 2.4846 >> 1.9884 2.3871 C 0 0 0 0 0 0 | 1.9120 -0.2779 0.8908 H 0 0 0 0 0 0 | >> 0.4143 0.6503 1.1018 H 0 0 0 0 0 0 | 1.1875 0.5634 -0.4904 H 0 0 0 0 0 0 >> | 1.6488 2.7601 0.5641 H 0 0 0 0 0 0 | 3.1383 1.8388 0.3457 H 0 0 0 0 0 >> 0 | 1.5564 2.0516 2.9643 H 0 0 0 0 0 0 | 3.0724 2.8892 2.5888 H 0 0 0 0 >> 0 0 | 3.0534 1.1241 2.7448 H 0 0 0 0 0 0 | 1 2 1 0| 1 4 1 0| 1 5 1 0| 1 >> 6 1 0| 2 3 1 0| 2 7 1 0| 2 8 1 0| 3 9 1 0| 3 10 1 0| 3 11 1 0|M END|> >> |-4.897042|||" >> >> Otis >> >> -- >> Otis Rothenberger >> chemagic.com >> >> >> >> >> >> -- >> >> ___ >> 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 > > > -- > > > > > ___ > Jmol-users mailing > listjmol-us...@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users > > > -- > Otis Rothenbergerchemagic.com > > > > -- > > > ___ > 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] SMILES
On Mon, May 31, 2010 at 9:52 PM, Otis Rothenberger wrote: > Bob, > > OK, I got it: > > 1. The url has to be encoded. > 2. Which I tried before I wrote using ASP.NET UrlEncode > 3) Hand entry of CCC%23C below works. > 4) ASP.NET must be choking on "#" with Server.UrlEncode() The # has a special meaning in URLs with form submissions. I am sure that is why it has to be urlencoded. Miguel -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] surface representations of atom selections
Check the documentation regarding the isosurface command and the options
SELECT and IGNORE. Some combination of those two will do exactly what you
want. If you use SASURFACE and you want the same scale as geosurface or dots
or spacefill, be sure to use SASURFACE 0.
Some reason not to just use spacefill? Or are you already using that within
a translucent surface?
I should probably remove the geosurface-dots motion business. It's not a
much-used shape, and I'm not sure it makes any real difference in rendering
speed.
Bob
On Tue, Jun 1, 2010 at 5:45 AM, Roni Gordon wrote:
> Hello,
>
> I'm trying to show the "shrink-wrapped" surface of a ligand in Jmol
> -- but it appears that "isosurface" will simply render the portion of
> the complete (i.e. all loaded models) solvent-accessible
> surface. For a partially buried ligand, this breaks the surface
> noticeably. "geoSurface" seems to be a close approximation, but it
> renders as "spacefill", and turns into "dots" during rotation.
>
> Is there an option to only consider the requested {atom-expression}
> when calculating the surface -- that is, as though no other atoms are
> present?
>
> Thanks,
>
> Roni
>
>
>
>
> --
>
> ___
> 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
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Re: [Jmol-users] set defaults pymol
First I've heard of it, though the last thing Warren and I were working on before his unfortunate demise last fall was exactly this. We were not optimistic that a general solution could be had. I hope they don't just try to do this totally on their own -- it requires some substantial understanding of the underlying principles of the programs -- which are considerably different. Warren and I were amazed at how two different approaches to a problem could be SO different fundamentally. (Add VMD) The main issue was that the people who really get into Pymol are often looking for the next cover of Nature (and don't realize that Jmol + POV-Ray options exist) or are working with its plug-in capability. They are not trying to actually communicate using 3D models the way Jmol users are. Or, to put it another way, there's not much of a common set of functionality here to work from. The basics are easy to replicate; the fine points are nearly impossible. But they certainly have my support. It's a noble goal. Bob 2010/6/1 Angel Herráez > I don't use Pymol, but that doesn't sound bad -as long as it is not > difficult to implement. > > By the way, I've recently known about an initiative to set a system > that translates between script languages: Pymol, Rasmol, Jmol are the > first targets. The idea is that you can use the scripting language > that you know in the other programs, and it will be converted. > > http://sbevsl.sourceforge.net/ > https://sourceforge.net/projects/sbevsl/ > > > > > -- > > ___ > 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] rocketBarrels and arrows head
If programs that remove the arrow heads from the helix cylinders also remove the heads from the sheet boxes, then Jmol should do that, too. What does Pymol do? 2010/6/1 Angel Herráez > El 1 Jun 2010 a las 7:37, jaime.prilu...@weizmann.ac.il escribió: > > > It seems that this only works on alpha helices, no effect on beta sheets. > > What Bob meant is that he could expand the existing command so that > it affects beta sheets too. > > I have no opinion about whether this should be done or not. I think > that somebody asked time ago for the ability to remove the arrows > from the rocket cylinders. A similar issue may be raised regarding > the use or absence of arrowheads in helical stretches of ribbons > and/or cartoons -some programs put them in, some don't. > > > > > -- > > ___ > 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] surface representations of atom selections
Hello,
I'm trying to show the "shrink-wrapped" surface of a ligand in Jmol
-- but it appears that "isosurface" will simply render the portion of
the complete (i.e. all loaded models) solvent-accessible
surface. For a partially buried ligand, this breaks the surface
noticeably. "geoSurface" seems to be a close approximation, but it
renders as "spacefill", and turns into "dots" during rotation.
Is there an option to only consider the requested {atom-expression}
when calculating the surface -- that is, as though no other atoms are present?
Thanks,
Roni
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Re: [Jmol-users] Water related questions
According to "Angel Herráez" : > > Is there an option for drawing water as crosses instead of spheres? > There is "stars". I think you could use it for what you want. > If I remember correctly, Eric uses it in FirstGlance in Jmol. Thanks. Stars are ok but it seems that the size (stars 2.0) only affects the length of the lines, not its weight. Any way of controlling that as well? -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| R&D Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Water related questions
According to "Angel Herráez" : > > connect (water)(water) delete Great, thanks. This works perfect. Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| R&D Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] rocketBarrels and arrows head
El 1 Jun 2010 a las 7:37, jaime.prilu...@weizmann.ac.il escribió: > It seems that this only works on alpha helices, no effect on beta sheets. What Bob meant is that he could expand the existing command so that it affects beta sheets too. I have no opinion about whether this should be done or not. I think that somebody asked time ago for the ability to remove the arrows from the rocket cylinders. A similar issue may be raised regarding the use or absence of arrowheads in helical stretches of ribbons and/or cartoons -some programs put them in, some don't. -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] set defaults pymol
I don't use Pymol, but that doesn't sound bad -as long as it is not difficult to implement. By the way, I've recently known about an initiative to set a system that translates between script languages: Pymol, Rasmol, Jmol are the first targets. The idea is that you can use the scripting language that you know in the other programs, and it will be converted. http://sbevsl.sourceforge.net/ https://sourceforge.net/projects/sbevsl/ -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Water related questions
Sorry, I mixed up the syntax. it's connect (water)(water) delete -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Water related questions
> Is there an option for drawing water as crosses instead of spheres? There is "stars". I think you could use it for what you want. If I remember correctly, Eric uses it in FirstGlance in Jmol. > Is there an option to 'set autobond OFF' only for water? Don't think so, but maybe you can use "connect select(water) delete" to remove the bonds. -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
