Thanks Angel and Xavier for your help on my question of rotating one file while keeping another fixed. I have one quick last question. The description for the rotateSelect command states: "In addition, if the keyword SPIN is used, the command starts only the atoms spinning." I was wondering if there are combinations of commands that would follow rotateSelect and would allow the equivalent of spinSelect or moveSelect. I'd like to carry out a continuous rotation over a few seconds on one file (while keeping the other fixed) instead of a visually instantaneous rotation. Thanks again Henry Jakubowski
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Sunday, April 06, 2008 2:49 PM To: [email protected] Subject: Jmol-users Digest, Vol 23, Issue 6 Send Jmol-users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/jmol-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of Jmol-users digest..." Today's Topics: 1. multiple bonds and lone pairs (Xavier Prat-Resina) 2. Re: Displaying two files/models while fixing one and rotating the other ( Angel Herr?ez ) 3. script file names (again) and persistence? (Thomas Stout) 4. Bug: Unable to exit from loop (Eric Martz) 5. Fwd: script file names (again) and persistence? (Thomas Stout) 6. multiple bonds and lone pairs (Xavier Prat-Resina) 7. Unwanted hover report (Eric Martz) 8. A Jmol wiki with scene authoring tools: Proteopedia.Org (Eric Martz) ---------------------------------------------------------------------- Message: 1 Date: Sat, 5 Apr 2008 07:06:22 -0700 From: "Xavier Prat-Resina" <[EMAIL PROTECTED]> Subject: [Jmol-users] multiple bonds and lone pairs To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Jmol-users, Is there a way to tell Jmol to calculate automagically the multiple bonds and showing the corresponding lone pair lobes? (my molecule files lack the multiple bond information) As far as I know those two properties are not related in Jmol. I've been using "connect aromatic modify;calculate aromatic" for double bonds, but then I have to add the lone pairs manually and accordingly. Is there a way to do that with triple bonds by the way? e.g. N2 For example. in CO3(2-) there is (in the most stable resonance form) one double bond C=O and two single bonds. So the number of lone pairs is different in different oxygens. Thanks Xavier -- Xavier Prat-Resina Research Associate Journal of Chemical Education and University of Wisconsin 209 N. Brooks St. Madison, WI 53715-1116 Tel: 608 8901702 // Fax: 608 2627145 e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat http://x.prat.resina.googlepages.com ------------------------------ Message: 2 Date: Sat, 05 Apr 2008 17:30:05 +0200 From: " Angel Herr?ez " <[EMAIL PROTECTED]> Subject: Re: [Jmol-users] Displaying two files/models while fixing one and rotating the other To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=US-ASCII Hi Henry Not sure if I have your setup right, but I tried this and it works: load leu.pdb load append butane.pdb frame all select */2 rotateSelected Y 90 ------------------------------ Message: 3 Date: Sat, 5 Apr 2008 14:00:30 -0700 From: "Thomas Stout" <[EMAIL PROTECTED]> Subject: [Jmol-users] script file names (again) and persistence? To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" I've been doing (more) development of a web page using jmol & thank you again for all of the guidance of a couple weeks ago - it's been very helpful! I've run into two more "oddities", which I am sure derive from my lack of in-depth knowledge. 1) Is there a limit to the length of a script file name? I've found that calls to a script named something like "protein_ligand_water_measure.spt" do not execute, while renaming the same file to "A_Z_Wdist.spt" works just fine. It's not a big deal, I can easily use shorter file names but I am curious as to what the string length limit is.... 2) Is there memory persistence within a browser? When testing, I have been making changes in scripts files and then re-calling that file from the web page but it appears that the old version of the script file continues to be executed, even when the page is re-loaded. The only way I've found to access the new version of the script file to fully close the page (or tab) containing the applet and re-access the web page. I've found this to be true using both Firefox and the dreaded IE on WinXP and linux (RHEL). Thanks! -Tom -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 4 Date: Sun, 06 Apr 2008 11:52:51 -0400 From: Eric Martz <[EMAIL PROTECTED]> Subject: [Jmol-users] Bug: Unable to exit from loop To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Bob, We are trying to exit from a loop that Frieda Reichsman has used extensively without problems. However it is not working in applet 11.5.24. It does work in the version Frieda used, 10.9.98, and also in 11.5.5_dev. So we suspect a new bug in 11.5.24 that was introduced since 11.5.5_dev. We want the molecule to rock until the user stops rocking with an exit command. The rocking script is: set hermitelevel 0 spin off delay 0.2 move 0 -30 0 0 0 0 0 0 3.0 delay 0.2 move 0 30 0 0 0 0 0 0 3.0 delay 0.2 loop on When we paste the above script into the console and execute it, the molecule rocks. When we type "exit" in the console of 11.5.24 and execute it, most of the time the console reports "pending" but rocking continues indefinitely. Occasionally, the exit stops the rocking, but we can't see a pattern to when it works. "exit" works 100% of the time in 11.5.5_dev and 10.9.98. Thanks, -Eric ------------------------------ Message: 5 Date: Sun, 6 Apr 2008 10:25:26 -0700 From: "Thomas Stout" <[EMAIL PROTECTED]> Subject: [Jmol-users] Fwd: script file names (again) and persistence? To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" This seems to have gone into the bit bucket the first time I sent it.... -Tom ---------- Forwarded message ---------- From: Thomas Stout <[EMAIL PROTECTED]> Date: Sat, Apr 5, 2008 at 2:00 PM Subject: script file names (again) and persistence? To: [email protected] I've been doing (more) development of a web page using jmol & thank you again for all of the guidance of a couple weeks ago - it's been very helpful! I've run into two more "oddities", which I am sure derive from my lack of in-depth knowledge. 1) Is there a limit to the length of a script file name? I've found that calls to a script named something like "protein_ligand_water_measure.spt" do not execute, while renaming the same file to "A_Z_Wdist.spt" works just fine. It's not a big deal, I can easily use shorter file names but I am curious as to what the string length limit is.... 2) Is there memory persistence within a browser? When testing, I have been making changes in scripts files and then re-calling that file from the web page but it appears that the old version of the script file continues to be executed, even when the page is re-loaded. The only way I've found to access the new version of the script file to fully close the page (or tab) containing the applet and re-access the web page. I've found this to be true using both Firefox and the dreaded IE on WinXP and linux (RHEL). Thanks! -Tom -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 6 Date: Sun, 6 Apr 2008 10:47:47 -0700 From: "Xavier Prat-Resina" <[EMAIL PROTECTED]> Subject: [Jmol-users] multiple bonds and lone pairs To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Jmol-users, Is there a way to tell Jmol to calculate automagically the multiple bonds and showing the corresponding lone pair lobes? (my molecule files lack the multiple bond information) As far as I know those two properties are not related in Jmol. I've been using "connect aromatic modify;calculate aromatic" for double bonds, but then I have to add the lone pairs manually and accordingly. Is there a way to do that with triple bonds by the way? e.g. N2 For example. in CO3(2-) there is (in the most stable resonance form) one double bond C=O and two single bonds. So the number of lone pairs is different in different oxygens. Thanks Xavier -- Xavier Prat-Resina Research Associate Journal of Chemical Education and University of Wisconsin 209 N. Brooks St. Madison, WI 53715-1116 Tel: 608 8901702 // Fax: 608 2627145 e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat http://x.prat.resina.googlepages.com ------------------------------ Message: 7 Date: Sun, 06 Apr 2008 14:20:21 -0400 From: Eric Martz <[EMAIL PROTECTED]> Subject: [Jmol-users] Unwanted hover report To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii"; format=flowed In applet 11.5.24 we are getting an unwanted hover report when we use the state script. The state script was obtained via jmolScriptWaitAsArray("show state", "appletId"). The hover was not showing when the state script was obtained. Further, it appears that the hover report is always for an atom present in the upper left corner of the applet view square. An example can be seen in the initial view here: http://proteopedia.org/wiki/index.php/Nucleosomes (the hover for Lys27 appears at the upper left after the moveto is done). The unwanted hover report appears unchanged, even after new scripts are executed, until one clicks in Jmol. It then disappears. We have tried adding "hover off" to the end of the script, but when we turn hover back on in the next line, the unwanted report appears, despite the mouse not being in (and never having been in) this jmol. Thanks, -Eric ------------------------------ Message: 8 Date: Sun, 06 Apr 2008 15:48:38 -0400 From: Eric Martz <[EMAIL PROTECTED]> Subject: [Jmol-users] A Jmol wiki with scene authoring tools: Proteopedia.Org To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii"; format=flowed http://Proteopedia.Org is a new Jmol-based server developed by Joel L. Sussman (an eminent crystallographer and former Head of the Protein Data Bank), Jaime Prilusky (author of The OCA PDB Browser and Head of the Bioinformatics Unit at the Weizmann Institute), and Eran Hodis (developer of the eMovie PyMol plugin for macromolecular movie making) at the Weizmann Institute in Israel. I think it is one of the most exciting uses of Jmol that I have seen -- perhaps the most exciting. Proteopedia is a wiki on macromolecular structure, so anyone can contribute (as in Wikipedia). Its most exciting innovation is a "Scene Authoring Tool" that makes it easy for those unfamiliar with the Jmol scripting language to develop custom molecular views, or scenes, in Jmol. These scenes are then automatically saved (as state scripts), and played back in Jmol from "green links" in the text. There can be as many applets per page as needed. You are invited to add text about your favorite molecules, to add scenes that show key features, and to suggest ideas for technical improvements to best exploit Jmol. It is expected that, as visitors add content, Proteopedia will develop into one of the most useful on-line reference sites for structural information about macromolecules. Proteopedia already contains an automatically-generated page for each of the nearly 50,000 entries in the Protein Data Bank. This automatic page contains the molecule in Jmol, with green links to display every site and ligand in the PDB file (echoing their full names), the abstract of the paper, and links to a few other particularly useful structure services and resources. Students and Educators can develop macromolecular structure tutorials in Proteopedia far more easily than in any other system at present. Proteopedia can also be used for supplementary materials for journal publications, or laboratory websites. For lecture presentations, supplementary materials or lab websites, those who contribute the content need to be able to guarantee that their pages will not be edited by others. Unlike Wikipedia, Proteopedia provides an easy solution. Each user has the option of creating protected pages that only s/he can edit. Others can copy, edit, and adapt the content from protected pages, since all content (including protected content) is bound to the GNU Free Document License. I recently taught a course to 40-some researchers in which I introduced Proteopedia. I had the entire class try out the scene authoring tools concurrently on their laptops. I assigned each student a number from one to 40 by counting and pointing. Each student then used (or created) a page "Sandbox N", where N is that student's number (for example, "Sandbox 15" for the student assigned number 15). As in Wikipedia, Sandbox pages are places to practice. Their content is periodically cleared. Proteopedia uses MediaWiki, and was greatly facilitated by Nico Vervelle's Jmol Extension. Have fun! -Eric ---- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz ------------------------------ ------------------------------------------------------------------------ - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Register now and save $200. Hurry, offer ends at 11:59 p.m., Monday, April 7! Use priority code J8TLD2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/j avaone ------------------------------ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users End of Jmol-users Digest, Vol 23, Issue 6 ***************************************** ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Register now and save $200. Hurry, offer ends at 11:59 p.m., Monday, April 7! Use priority code J8TLD2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
