[Jmol-users] Water related questions

Hi, Two water related questions: Is there an option for drawing water as crosses instead of spheres? Is there an option to 'set autobond OFF' only for water? Thanks, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| R&D

Re: [Jmol-users] rocketBarrels and arrows head

According to "Robert Hanson" : > I'm happy to remove arrow heads from the boxes with > set rocketbarrels true It seems that this only works on alpha helices, no effect on beta sheets. Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics

Re: [Jmol-users] SMILES

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() Otis On 5/31/2010 9:14 PM, Otis Rothenberger wrote: Bob, Do you have any idea why this is

Re: [Jmol-users] SMILES

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

Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model

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 AJA

Re: [Jmol-users] SMILES

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. Sinc

Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model

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

[Jmol-users] set defaults pymol

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 -- Robert M. Hanson Professor of Chemistry

Re: [Jmol-users] rocketBarrels and arrows head

I'm happy to remove arrow heads from the boxes with set rocketbarrels true Is it a common view to have no arrow heads at all? What does Pymol do? Bob On Mon, May 31, 2010 at 10:38 AM, wrote: > According to "Angel Herráez" : > > 'set rocketBarrels' is working OK for me in 11.8.23, 11.8.24

Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model

Bob, the SMILES support is really *fantastic*! In the conversion from SMILES -> 3D ... Q: ... are the atom locations more-or-less correct for a low-energy configuration? Q: ... are the bond angles more-or-less correct? Miguel ---

Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model

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 Her

Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model

Hello, you could also try to search it on the net, maybe in this site http://cdb.ics.uci.edu/cgibin/ChemicalSearchWeb.psp regards -Ursprüngliche Nachricht- Von: Miguel Howard [mailto:mig...@jmol.org] Gesendet: Montag, 31. Mai 2010 18:16 An: jmol-users@lists.sourceforge.net Betreff: [Jmo

Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model

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! --

Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model

Hi Miguel! You can draw it and have Jmol optimize 3D Or draw it elsewhere and optimize 3D (I use ChemSketch) then save and open in Jmol -- ___ Jmol-users mailing list Jmol

[Jmol-users] need 2-propenyl sulfenic acid molecular model

My son is doing a report on 2-propenyl sulfenic acid for his high school chemistry class. He would like to incorporate Jmol into his presentation ... and I think that is a good idea :) Q: Where can I get a file for 2-propenyl sulfenic acid? Thanks! Miguel --

Re: [Jmol-users] rocketBarrels and arrows head

According to "Angel Herráez" : > 'set rocketBarrels' is working OK for me in 11.8.23, 11.8.24, 12.0.RC11 > and 12.0.RC15 Thanks a lot. Will try again. Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| R&D Bioinformatics

Re: [Jmol-users] rocketBarrels and arrows head

Hi Jaime 'set rocketBarrels' is working OK for me in 11.8.23, 11.8.24, 12.0.RC11 and 12.0.RC15 > In general, is there an option to remove arrow heads? > (beta sheets, ...) I don't think so. But I see no reason to be able to remove arrowheads from alpha rockets and not from beta rockets.