Re: [Jmol-users] Jmol Java applet revocation explained

2015-10-17 Thread Jim Procter
Hi Bob.. On 17/10/2015 17:16, Robert Hanson wrote: Ah, but there is a catch. Despite the fact that the Jmol code was signed with a timestamp, revocation *prior to the expiration date of the certificate* results in Oracle's Java applet initializer to disregard the timestamp and not allow such

Re: [Jmol-users] RNA/DNA Secondary Structure, anyone?

2014-04-10 Thread Jim Procter
Hi Bob. I'm also interested, though I think you should be aiming big ;) The development build of Jalview (which will eventually be 2.8.2 by the summer) has an RNAView based secondary structure shading scheme that was developed by a summer student, Anne Menard, back in 2012. Currently, 2.8.2

Re: [Jmol-users] RNA/DNA Secondary Structure, anyone?

2014-04-10 Thread Jim Procter
Thanks for your interest Bob - lets see how far we can go ! On 10/04/2014 13:26, Robert Hanson wrote: Ah, yes, Jim. Looks like there are lots of possibilities here. Consider it done. What do I need to do to get you what you need? read on :) I opened Jalview, and loaded 2GIS; I don't see any

[Jmol-users] FINAL CALL: Jalview course + workshop at Oxford, Dec 12-13th

2013-12-02 Thread Jim Procter
Thanks - and please forward this to people in your institute who might be interested! Jim Procter. -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how

[Jmol-users] Less than 24 hours to submit a poster to VIZBI 2013

2013-03-14 Thread Jim Procter
for submitting posters are included in your registration email. If you aren't registered yet, go to: http://vizbi.org/2013/Registration/ We also have a few places left for the VIZBI tutorial day. Take a look at the great sessions on offer at http://vizbi.org/2013/Program/ See you in Boston next week! Jim

Re: [Jmol-users] viewing structures contained in jar archives with the Jmol applet

2011-03-07 Thread Jim Procter
On 07/03/2011 12:12, Angel Herráez wrote: Jim, since a JAR is a zipfile, I'd say that you just need the same syntax as for loading a JMOL or ZIP file. Maybe it's LOAD ... FILTER. Check the scripting doc thanks ! I was looking with google, rather than using the reference .. doh :) From

Re: [Jmol-users] viewing structures contained in jar archives with the Jmol applet

2011-03-07 Thread Jim Procter
On 07/03/2011 12:44, Jim Procter wrote: On 07/03/2011 12:12, Angel Herráez wrote: Jim, since a JAR is a zipfile, I'd say that you just need the same syntax as for loading a JMOL or ZIP file. Maybe it's LOAD ... FILTER. Check the scripting doc thanks ! I was looking with google, rather

Re: [Jmol-users] Accessing Secondary Structure assignments: Re: Jmol and DSSP

2010-10-12 Thread Jim Procter
On 12/10/2010 12:07, Gert Vriend wrote: Ls, The group of Steve Pettifer in Manchester has a DSSP Web service (findable through the EMBRACE Web service registry: http://www.embraceregistry.net/). At the CMBI you can find an interpreted DSSP Web service through WHAT IF

Re: [Jmol-users] Accessing Secondary Structure assignments: Re: Jmol and DSSP

2010-10-12 Thread Jim Procter
On 12/10/2010 13:02, Robert Hanson wrote: Ah, yes. Forgot to mention that. There's a new atom property called substructure : print {*.ca}.substructure.all # numbers 0 through 8 select substructure=7 # just the 3/10 helices select {*.ca}; label %[substructure] # words helix,