Have sorted out the problem. Just needed to add the ‘offset 1.4’ to command  (The SurfaceColor dialog panel has a surface offset parameter (default value of 1.4 gives the ‘smearing’ effect I mentioned – essentially has the effect of colouring the molecular surface as though it is a solvent-accessible surface)……..

From: Ashley Pike
Sent: 28 September 2012 19:02
To: 'Tom Goddard'
Cc: chimera-users@cgl.ucsf.edu
Subject: RE: [Chimera-users] Specifying colour of surface cap when surface coloured by electrostatic potential

OK I see. This gives me a single colour clipped cap *BUT* the colouring of my surface is now very different from the result I see when colouring using the SurfaceColor dialog panel (with the same values -10,0,10). The colours generated by the suggested command are very intense rather than smeared out. For example a hydrophobic surface when coloured via the panel appears virtually white when coloured according to electrostatic potential (what one would expect) but from command line the same region appears as a patchwork of red/white and blue? I suspect some scaling is going on when colouring invoked from command line? I have played with qualifier ‘cmapRange full’ but this doesn’t seem to do the job.

From: Tom Goddard [mailto:goddard@sonic.net]
Sent: 28 September 2012 17:34
To: Ashley Pike
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] Specifying colour of surface cap when surface coloured by electrostatic potential

Hi Ashley,

  You can get a single color clipped cap by doing the electrostatic surface coloring with a command

    scolor #0 volume #1 cmap -10,red:0,white:10,blue  autoUpdate false

where #0 is the molecular surface and #1 is the electrostatic map (*.dx file).  The key here is the "autoUpdate false" option.  That means the coloring on the clip surface won't be updated as the clip plane is moved.  The above command will still color the current clip surface and you'll have to move the clip plane to make it a single color.  The Surface Color dialog does not offer control over the "autoUpdate" option so it can only be done with a command.

    Tom

Hi – Can’t find answer to this question in manual. Is it possible to assign a uniform solid colour to a surface cap when the (clipped) surface is coloured by electrostatic potential (using external .dx file)? I know such capping can be done when the surface is coloured by some other attribute but have not found a way to specify in the above case.

Any hints gratefully received.

Many thanks,

Ashley

--

Dr. Ashley Pike

Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford

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