export figure from Jmol

Jalview Discussion
1

Dear all

I have been using Jalview to perform a sequence alignment on a protein for which I have a structure. This produces a figure in Jmol which colours the structure by conservation. This is a great feature, but Jmol isn't great for producing publication quality figures. I was wondering if its possible to output the pdb file from Jmol with the conserved residues labelled in some way, for example in the B factor column of the pdb file.

Thanks

John

···

--
John Berrisford

Medical Research Council
Mitochondrial Biology Unit
Wellcome Trust / MRC Building
Hills Road
Cambridge
CB2 0XY
WEB: www.mrc-mbu.cam.ac.uk
TEL: +44 (01223) 252918

2

The latest Jmol versions allow exporting images as povray files that can produce high quality images. They can also render images internaly with antialiasing option.
If you’d like to do that, you should download the latest jmol release from :
http://chemapps.stolaf.edu/jmol/

  • In Jalview, open the jmol console and enter the following script :
    show history
    copy the given script

  • In the latest jmol release (start jmol.jar), load the pdb file you want. paste the script in the console and edit it to remove the load command issued by jalview.

  • execute the script : you should have the same output as the one provided by jalview.

  • the command “set antialiasdisplay true” would produce an antialiased image. the command “set hermitelevel 10” would give better looking ribbons.

  • you can export the image directly as a png/jpg file, see : http://chemapps.stolaf.edu/jmol/docs/#writeimage,frames

  • or you can export the scene as a povray project : write povray “myfilename.pov” This will provide you with a povray scene description file (pov extension) and a povray setting file (ini extension). You can then use that last file with the povray program to create your image.

Paul

···

Le 4 mars 2010 à 14:01, John M. Berrisford a écrit :

Dear all

I have been using Jalview to perform a sequence alignment on a protein
for which I have a structure. This produces a figure in Jmol which
colours the structure by conservation. This is a great feature, but Jmol
isn’t great for producing publication quality figures. I was wondering
if its possible to output the pdb file from Jmol with the conserved
residues labelled in some way, for example in the B factor column of the
pdb file.

Thanks

John

–
John Berrisford

Medical Research Council
Mitochondrial Biology Unit
Wellcome Trust / MRC Building
Hills Road
Cambridge
CB2 0XY
WEB: www.mrc-mbu.cam.ac.uk
TEL: +44 (01223) 252918

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