[Jmol-developers] [ jmol-Bugs-1297760 ] ssbonds on/off
Bugs item #1297760, was opened at 2005-09-21 07:06 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1297760&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Scripting Group: None Status: Open Resolution: None Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Miguel (migueljmol) Summary: ssbonds on/off Initial Comment: Maybe I mentioned this already, but SSBONDS OFF does not work until an SSBONDS ON command is given, even though the disulfide bonds are displayed by default. Bob Hanson -- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1297760&group_id=23629 --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] [ jmol-Bugs-1297762 ] set radius ?
Bugs item #1297762, was opened at 2005-09-21 07:08 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1297762&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: set radius ? Initial Comment: set radius n.m does not work. I believe this was supposed to be a replacement for set solvent n.m which (as previously noted) does not work either. I would prefer if "set radius" were correct. Bob Hanson -- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1297762&group_id=23629 --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] Re: color (what else)? set radius
> In Eval.java there is > > set radius (decimal number) > > and I thought before this was > > set solvent (decimal number) > > But I can't get either of those to work. How does one set the solvent > probe > radius for DOTS? Well, it is not easy ... it is a combination of the two. You change the radius using set radius But, you have to turn on the solvent using set solvent on load "samples/xyz/caffeine.xyz"; dots on; # vdw dots set solvent on; dots off; dots on; # default solvent radius set radius 3.0; # bigger radius dots off; dots on; # must turn off and on in order to force recalc set radius 0.5; dots off; dots on; # smaller radius The combination of 'solvent' and 'radius' was driven by rasmol compatibility. However, at this point it deserves a second look. If/when I get solvent-accessible surfaces working I may fold the dots support into that, changing the 'dots' commands as I do so. Miguel - Open Source Molecular Visualization www.jmol.org [EMAIL PROTECTED] - --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] [ jmol-Bugs-1298218 ] show file bug
Bugs item #1298218, was opened at 2005-09-21 15:43 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1298218&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Scripting Group: None Status: Open Resolution: None Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Miguel (migueljmol) Summary: show file bug Initial Comment: Ha, ha (sorry, this is just a funny action): after a loadInline() of data to the Jmol applet, show file returns the file "string" in the directory containing the web page. Go ahead and try this at http://fusion.stolaf.edu/chemistry/jmol/loaddata.htm 1) Load "1crn" (this occurs using the loadInline() function 2) enter "show file" on the command line and press "Run" correct action should be to display the loadInline() string itself, not the file named "string" Bob Hanson -- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1298218&group_id=23629 --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
