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

Jim Procter jprocter at compbio.dundee.ac.uk
Fri Jan 13 18:00:27 GMT 2012


Hello Hari.

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



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