[Jmol-users] RotateSelected
Hello, I tried to use the RotateSelected function, but it doesn't work. In the documentation I found a remark V. 11.2 - new, but the newest stable version to download is 11.0.3, and I cannot believe that the documentation ist earlier online than the program. So my questions : Can I get version 11.2 from somewhere, or if not, when will it be ready ? Or may there be other reasons that the use of the RotateSelected command failed ? Thanks Michael Schmidt - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] size of ions
Hello, I want to display a NaCl crystal. So I loaded a pdb file that contains lines like this : HETATM1 Na1 1 -2.820 -2.820 -2.820 1.00 0.00 NA1+ ... ... HETATM 33 Cl1 1 0.000 -2.820 -2.820 1.00 0.00 CL1- I expected to see the Na ions having about half the size of the Cl ions, but Jmol produced output where Na ions were greater than the Cl ions. They seemed to be Na and Cl atoms rather than ions. So I tried to give them the proper charge in the load script load nacl.pdb; select atomno33; formalCharge=1; select atomno32; formalCharge=-1; but nothing changed. Then I loaded some cif files, and I looked at the example page fractional coordinates, and always saw atom-sized balls rather than ion-sized. My question : How can I produce Jmol output where the ions have ionic radii, not atomic radii ? I work with Jmol 11.2.14 and Windows XP. Thanks for any help. Michael - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] size of ions
My question : How can I produce Jmol output where the ions have ionic radii, not atomic radii ? spacefill IONIC Generates a sphere for each atom according to an approximation of its ionic radius. Thanks a lot ! Michael Schmidt - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] missing "console" window in windows 7 after using extended display
Dear All, This is just to report about what happened to me and might happen to others jmol windows users. Last night I discovered that the jmol "console" window would not open when I clicked on it in the menu. I've never seen that happening before, so I thought it could be a problem with either the latest jmol (14.15.2) or the latest java update (for windows 64). I reinstalled both jmol and java and even tried an old version of java, but nothing. Everything worked with exception of the console window. The script window was showing up, so I could just used that, but I was still puzzled. Thinking that the console window was maybe open but invisible I've tried to type a command and click enter and, surprise, the command worked, but no console was visible anywhere on the screen. Now, a week ago or so I was trying using an extended display with two monitors and I switched back to a single monitor after a day or two. Just for trying, I switched back the display to extended and here the Jmol console window appeared again... Never seen something like that. Every other application was working perfectly fine on both displays and in extended mode, and the PC was restarted several time, but somehow the display variable in Jmol was still stuck on the wrong display. Anyway, I leave this here in the hope it could help other people in the same situation. Sorry for the long email, Marco -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] ...still problems with the extended display...
Sorry, just to add the my previous email is that the problem of the console window not appearing after I switch back to a single display still persists... I tried everything, unplugging and uninstalling the other monitor, moving the jmol window from a monitor to another, but nothing, as soon as I close jmol and restart it, the console window goes to the wrong monitor...Any suggestions will be welcomed. Thanks, Marco-- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] ...still problems with the extended display...
Thanks. After few hours, I've just arrived at a similar solution. What I did is delete the content of the history file in .jmol and restart. Console window back. I didn't know about the different behaviour between close and exit and click on the windows though. Normally it doesn't matter too much, except in this case it would try to open the window out of the screen. Did you try moving the console to where you want it, then clicking Quit (or Close) from Jmol's pull-down File menu? On a Mac, this saves the window positions so the next time you start Jmol, they are remembered. In contrast, other methods of quitting (Jmol menu in the menubar, Quit; Cmd-Q) do NOT save the window positions. Not sure about Windows 7. On 5/9/17 6:03 AM, MS wrote: > Sorry, just to add the my previous email is that the problem of the > console window not appearing after I switch back to a single display > still persists... I tried everything, unplugging and uninstalling the > other monitor, moving the jmol window from a monitor to another, but > nothing, as soon as I close jmol and restart it, the console window > goes to the wrong monitor... > Any suggestions will be welcomed. > > Thanks, > > > Marco > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > ___ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users-- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
