[Jalview-discuss] clipping plane Jmol from within Jalview and export sequence-conservation color code as b-factor record?

hari jayaram harijay at gmail.com
Thu Jan 12 22:54:35 GMT 2012

Hi ,
Here is what I did.
1) Aligned two sequences  using Clustaw : sequence 1 corresponding to
a  pdb-id  and sequence-2 a closely related (60% sequence identity)
with no structure.
2) In Jalview I opened the aligned seuqence file , right clicked
sequence-2 and then associated it with the PDB id for the sequence 1
3) Now displaying the pdb  and coloring by sequence..colors all the
dissimilar parts in white and conserved sequence in lilac.

My Questions are

Is there a way to export the color code as a new pdb-file with the
color as a b-factor record?
I tried clipping the JMOL view using CTRL-SHIFT and click-drag-up-down
as suggested in the help. But the clipping pane didnt move. How do I
manipulate the clipping panes in JMOL

Thanks for your help

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