Re: [Jmol-users] Jmol displays NBOs in GAMESS and Gaussian

2009-10-30 Thread Robert Hanson
load h2so4_nbo.log filter "NBOCharges MO" model 2;label %P;mo 10 On Tue, Oct 27, 2009 at 6:38 PM, Xavier Prat-Resina wrote: > Thanks for the fast response Bob. > > I meant to have access to the NBO charges at the same time as the regular > MOs, > not the Natural Bond Orbitals. > I'm using the sam

Re: [Jmol-users] Jmol in web and stand alone different result to same actions

2009-10-30 Thread Rolf Huehne
Phil Cunningham wrote: > HI > I have a protein, 2 chaind displaye din Jmol window both on the web and > standalone > > on the web i use a script to select all Transmenebrane regions usng a > script Ior (reset them) > I intend to highligh or reset JUST the TM regions > > this is fine stand alon

Re: [Jmol-users] Jmol in web and stand alone different result to same actions

2009-10-30 Thread Phil Cunningham
Yes same version (a copy!) Phil Angel Herráez wrote: > Phil, the app (standalone) and applet (webpage) should do the same. > First, make sure you are using the same Jmol version in both. If it > is so, we can keep investigating. > > > > --

Re: [Jmol-users] Jmol in web and stand alone different result to same actions

2009-10-30 Thread Angel Herráez
El 30 Oct 2009 a las 16:52, Phil Cunningham escribió: > You can view my effort at > http://www.kcl.ac.uk/ip/philcunningham/christer/oct09/3h90.html > the all tm button is on the right hand side When I try that, checking "all tm" paintes them in red, unchecking paints them in grey. So I think it

Re: [Jmol-users] Jmol in web and stand alone different result to same actions

2009-10-30 Thread Robert Hanson
What are the two versions you are using? Oh, I see 11.6.25 there -- please upgrade the applet to 11.8. On Fri, Oct 30, 2009 at 11:52 AM, Phil Cunningham wrote: > HI > I have a protein, 2 chaind displaye din Jmol window both on the web and > standalone > > on the web i use a script to select a

Re: [Jmol-users] Jmol in web and stand alone different result to same actions

2009-10-30 Thread Angel Herráez
Phil, the app (standalone) and applet (webpage) should do the same. First, make sure you are using the same Jmol version in both. If it is so, we can keep investigating. -- Come build with us! The BlackBerry(R) Develope

Re: [Jmol-users] Can I get the Jmol content as CML?

2009-10-30 Thread Robert Hanson
Writing surface files -- with the latest build (not released as JAR yet) I recommend writing ".xjvxl" files -- this produces a valid XML version of the surface file that can be read with Jmol 11.9.7. Bob On Fri, Oct 30, 2009 at 9:32 AM, Rzepa, Henry wrote: > >On Fri, Oct 30, 2009 at 3:03 PM, Rz

[Jmol-users] Jmol in web and stand alone different result to same actions

2009-10-30 Thread Phil Cunningham
HI I have a protein, 2 chaind displaye din Jmol window both on the web and standalone on the web i use a script to select all Transmenebrane regions usng a script Ior (reset them) I intend to highligh or reset JUST the TM regions this is fine stand alone but within a web page my selection /col

Re: [Jmol-users] Can I get the Jmol content as CML?

2009-10-30 Thread Rzepa, Henry
>On Fri, Oct 30, 2009 at 3:03 PM, Rzepa, Henry wrote: >> As it happens, Bob and I have been having a discussion about eg saving XYZ >> (with >> vibrational vectors). Bob's documentation does describe the process, >> although of course >> one has to use the signed applet to use the write comm

Re: [Jmol-users] Can I get the Jmol content as CML?

2009-10-30 Thread Egon Willighagen
On Fri, Oct 30, 2009 at 3:03 PM, Rzepa, Henry wrote: > As it happens, Bob and I have been having a discussion about eg  saving  XYZ > (with > vibrational vectors).  Bob's documentation does describe the process, > although of course > one has to use the signed applet to use the write command if

Re: [Jmol-users] Can I get the Jmol content as CML?

2009-10-30 Thread Rzepa, Henry
>Hi all, > >is Jmol still able to save the content? For example as CML or perhaps >MDL molfile or XYZ? As it happens, Bob and I have been having a discussion about eg saving XYZ (with vibrational vectors). Bob's documentation does describe the process, although of course one has to use the s

[Jmol-users] Can I get the Jmol content as CML?

2009-10-30 Thread Egon Willighagen
Hi all, is Jmol still able to save the content? For example as CML or perhaps MDL molfile or XYZ? Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ---