Re: [Jmol-users] Jmol and Protein Explorer

Hi, I have tried several times to remove myelf from the mailing list, but to no avail. Any suggestions? Thanks, Mike -Original Message- From: Bob Hanson <[EMAIL PROTECTED]> To: jmol-users@lists.sourceforge.net Date: Tue, 03 Jun 2008 16:31:55 -0500 Subject: Re: [Jmol-users] Jmol and Pro

[Jmol-users] loading client-side files using signed jmol applet

Hi list, I was wondering if it's possible to load local files from the client side into the signed jmol applet without having to copy the file back to the server side first. I understand that the standard way is to upload the client's file to a temp directory on the server, and then have jmol a

Re: [Jmol-users] Jmol and Protein Explorer

On 3 Jun 2008 at 16:31, Bob Hanson wrote: > OK -- hbonds, contacts, surfaces -- I need to know what a "list" is in > Chime. "list" in Chime is a script command for a surface. The list is the name assigned to a surface when created using "surface", "load pmesh" or "load surface gaussian" command

Re: [Jmol-users] DRAW Charges on atoms + and -

Nick wrote. > Hi Angel, A very timely contribution. I was looking for a way to > showpositiveand negative > charges on atoms. > A few experiments later I find that > draw {atomno=4} "+" > draw {atomno=4} "-" > works quite nicely. Nick, why don't you use labels for that? select atomno=4; l

Re: [Jmol-users] Jmol and Protein Explorer

Karl Oberholser wrote: > Great work Bob. Several comments. When working in Quickviews and > making selections from the menus, the Busy indicator comes on, but the > change in the display or color does occur. After a couple occurrences > of this an error message is given in the message box, '

[Jmol-users] DRAW Charges on atoms + and -

Hi Angel, A very timely contribution. I was looking for a way to show positive and negative charges on atoms. A few experiments later I find that draw {atomno=4} "+" draw {atomno=4} "–" works quite nicely. Control over the colour and font size would be great and Bob suggested that Unicode

Re: [Jmol-users] << Plotting MEP from GAMESS >>

I don't know a lot about MEP, but the basic idea is that you need an n x n x n grid of charge values. Jmol will construct this grid if given point charges just using a simple q1q2/r idea, but I am not certain that that is the best way. So look for a) a list of atomic charges that are used as th

Re: [Jmol-users] Jmol and Protein Explorer

Great work Bob. Several comments. When working in Quickviews and making selections from the menus, the Busy indicator comes on, but the change in the display or color does occur. After a couple occurrences of this an error message is given in the message box, 'Error: busy_count=x. Even after th

[Jmol-users] << Plotting MEP from GAMESS >>

Hi everyone, I would like to know how to plot the Electrostatic Molecular Potential from calculations using GAMESS family (GAMESS, PC GAMESS, WinGAMESS). I read the GAMESS documentation and there is a group ($ELPOT) to calculate the electrostatic potential. In the output I have info about the tot

Re: [Jmol-users] NullPointerException while loading a PDB File

On Tue, Jun 03, 2008 at 12:44:06AM -0500, Bob Hanson wrote: > OK, that's fixed for 11.5.39. At least for the JmolSimpleViewer > interface, it could be fixed. (I don't know if that is what you are > using or not.) > > Mostly, though, it is a result of not calling > > viewer.evalString("ZAP");