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

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
Hari

Hello Hari.

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?

Not really. I took a look at the code, and there really isn't a simple way of doing this in Jalview due to the way it handles structures. Jalview only reads PDB structure data to determine the sequence with coordinates - and nothing else; in fact, the 'save PDB file' function simply dumps the file that Jalview was given.

The simplest approach might be to try and do this with Jmol's own scripting interface.
Documentation here (http://chemapps.stolaf.edu/jmol/docs/#atomproperties) suggest you can access and modify the bfactor and colour attributes for atoms in a loaded model. So, just open the Jmol console (right click on the window and select 'console'). Then do:

{*.*}.temperature={*.*}.color
select all;
write pdbwithtempfactors.pdb

This will write out a pdb file called 'pdbwithtempfactors.pdb' with modified temperature factors. What Jmol actually puts in the temperature factor is another matter! Hopefully it'll be enough for what you need.

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

ah. you're right - it looks like mouse events aren't getting to Jmol. Bug has been filed: http://issues.jalview.org/browse/JAL-1042
I'm afraid for this version of Jalview, you'll have to use the 'slab' command in the Jmol console to adjust the depth and position, which is somewhat painful. Sorry about that.

Jim.

ยทยทยท

On 12/01/2012 22:54, hari jayaram wrote: