Feature #313
closedImplement Jmol into webviewer of volumes
Added by Neil Voss about 14 years ago. Updated over 9 years ago.
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Updated by Neil Voss about 14 years ago
I asked the Japanese version of EMDB how they visualize electron density files in Jmol:
I am making JVXL files as follows. 1. comvert ccp4 map to 'obj' format data with UCSF Chimera. Chimera command: export format OBJ foo.obj 2. modify the obj file for Jmol. Jmol seems be able to read only 'v' and 'f' lines. 2-1. remove the header and comment lines, such as '#', 'vn', 'g', 'usemtl', and 'mtllib' lines. regexp: '^(#|vn|g|usemtl|mtllib) .+\n' => '' 2-2 replace '1234//1234' with '1234' in 'f' lines. regexp: '\/\/[0-9\.]+' => '' 3. export to JVXL format by Jmol. (This may not be necessary for your purpose, but is helpful to reduce the size of the data) Jmol command: isosurface obj "foo.obj"; write isosurface "foo.jvxl";
Updated by Neil Voss almost 14 years ago
- Target version set to Appion/Leginon 2.1.0
Updated by Amber Herold almost 14 years ago
- Target version changed from Appion/Leginon 2.1.0 to Appion/Leginon Future Version
Updated by Neil Voss almost 14 years ago
- Status changed from Assigned to New
- Assignee deleted (
Neil Voss)
I make the OBJ file for each volume using apChimera.renderSnapshots, but I cannot get the Jmol plugin to read files in the non-local directories, i.e., if the OBJ file is in myami/myamiweb/processing/groel.obj.gz then it works fine, but if the file is in /ami/data00/appion/06jul12a/groel.obj.gz it will not load. The Documentation says it should load if you are using the signed version of the program (for security reasons), but I could not get it to work.
See the Jmol website for docs and info: http://jmol.sourceforge.net/
Updated by Neil Voss about 13 years ago
- Assignee set to Amber Herold
- Priority changed from Low to Normal
Hi Amber/Eric, I ran across some document on Jolecule, I think this might be a better solution. The main problem I ran into is that some of our volumes are enormous in size and Java really sucks a ton of memory. I setup Chimera to prepare this data surface data (since it cannot display volume data), but I was having trouble getting to read files not in the myamiweb folder using the signed Jmol applet because of some sort of security reasons.
http://jmol.sourceforge.net/
http://wiki.jmol.org/index.php/Jmol_Applet
Check out my other site, where I had it working (seems broken now):
http://3vee.molmovdb.org/jmolViewer.php?objfile=output/11may10/747/11may10.747.obj.gz
Updated by Amber Herold about 13 years ago
Thanks for the update Neil. FYI, Friday will be Eric's last day at AMI.