Dear Bob, > It's just that the command is "axes" not "axis"
Thanks a lot for your loop examples & sorry for "axes" vs "axis"... @ http://q4md-forcefieldtools.org/RED/index-test.php, using a Tripos mol2 file format, you have a working example with: FF atom types + atomic charges + atom names + MEP using Jmol 11.7.6 All is perfect ! I will now make this more general on our web sites... > Francois, I'm starting to see where having atom types in more than mol2 > files is of interest. You posted something about that. Yes, in the CML file format (besides the Tripos mol2 file format). Angel wrote: >>> That would depend on the official specification of the CML format. >>> Jmol can be adapted to read anything the file contains, but it must >>> be defined as an official format spec. >> Yes, this is my understanding: so how to define a specific card for >> force field atom type in the CML file format recognized by Jmol: >> >> For charges, Jmol recognizes: >> <scalar dictRef="jmol:charge">-0.287</scalar> >> Could we imagine, something similar for force field atom types such as: >> <scalar dictRef="jmol:forcefield">CT</scalar> ? > Where are these cml files coming from? Tripos mol2 files from R.E.D. http://q4md-forcefieldtools.org/RED/ --> CML files for R.E.DD.B. http://q4md-forcefieldtools.org/REDDB/ using a perl script, I wrote: See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#15 & http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#17 http://q4md-forcefieldtools.org/Tutorial/0-Script/mol2tocml.pl > Peter can tell us what the story is > on adding something like atom type to the cml specification. Can you send us > one of these CML files to look at? You have many examples of CML files in R.E.DD.B. See for instance complex projects in R.E.DD.B.: http://q4md-forcefieldtools.org/REDDB/up/W-46/ or http://q4md-forcefieldtools.org/REDDB/up/F-60/ regards, Francois > On Fri, Oct 31, 2008 at 4:33 PM, FyD <[EMAIL PROTECTED]> wrote: > >> Dear All, >> >> I use Jmol 11.6.1. under fedora linux 32-bits with Opera 9.61. >> >> If I use the following script, the corresponding loop works fine: >> >> jmolApplet(200, "load ./DMSO1.cml; set echo top left;color echo >> black;font echo 10 serif bold;echo Atomic charges;select all;label >> %-8.3P;font label 10 serif bold;zoom 120; spin on; delay 5; load >> ./DMSO2.cml; set echo top left;color echo black;font echo 10 serif >> bold;echo Force field atom types;select all;label %B;font label 10 >> serif bold;zoom 120; spin on; delay 5; load ./DMSO3.cml; set echo top >> left;color echo black;font echo 10 serif bold;echo Atom names;select >> all;label %a;font label 10 serif bold;zoom 120; spin on; delay 5; loop >> 1") >> > > Interesting loop -- this is perhaps a bit cleaner: > > load caffeine.xyz > > message _loop > set echo top left > color echo black > font echo 10 serif bold > echo Atomic charges > select all > label %-8.3P > font label 10 serif bold > zoom 120 > spin on > delay 5 > > set echo top left > color echo black > font echo 10 serif bold > echo Force field atom types > select all > label %B > font label 10 serif bold > zoom 120 > spin on > delay 5 > > set echo top left > color echo black > font echo 10 serif bold > echo Atom names > select all > label %a > font label 10 serif bold > zoom 120 > spin on > delay 5 > goto _loop > > >> If I add 3 times the "axis 0.01" command in the loop, the loop does >> not start/work: >> >> jmolApplet(200, "load ./DMSO1.cml; axis 0.01; set echo top left;color >> echo black;font echo 10 serif bold;echo Atomic charges;select >> all;label %-8.3P;font label 10 serif bold;zoom 120; spin on; delay 5; >> load ./DMSO2.cml; axis 0.01; set echo top left;color echo black;font >> echo 10 serif bold;echo Force field atom types;select all;label >> %B;font label 10 serif bold;zoom 120; spin on; delay 5; load >> ./DMSO3.cml; axis 0.01; set echo top left;color echo black;font echo >> 10 serif bold;echo Atom names;select all;label %a;font label 10 serif >> bold;zoom 120; spin on; delay 5; loop 1") >> >> Same problem with adding 3 times "isosurface molecular map MEP; color >> isosurface translucent;" >> >> On the contrary, with "boundbox", the loop works fine. >> >> Any idea why ? >> >> Thanks, regards, Francois ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
