This is more half an answer than the real deal, but when I had the same issue I opted for the quick work around of setting the range from -100 to 100 for the blue-white-red palette which effectively made 0-100 correspond to white to red only since there were no negative B factors/conservation scores.
e.g.
spectrum b, blue_white_red, minimum=-100, maximum=100

I am curious for better answers, as you are, but haven't delved into the code to look for it myself, either. But perhaps this or some fine tuning of the range or other pre-defined palettes will get done what you desire.

Cheers,
Seth



Message: 1
From: Alexander.Pautsch@bc.boehringer-ingelheim.com
To: pymol-users@lists.sourceforge.net
Date: Fri, 30 Dec 2005 10:24:10 +0100
Subject: [PyMOL] new spectral color palette

This message is in MIME format. Since your mail reader does not understand
this format, some or all of this message may not be legible.

------_=_NextPart_001_01C60D22.CA0F1A47
Content-Type: text/plain
Content-Transfer-Encoding: 7bit

Hi

I would like to color my protein according to B-factor with a self-defined
spectral palette (In this case I have put sequence conservation into the
Bfactor this column). I found that
        spectrum b, blue_white_red, minimum=0, maximum=100
would do part of the job with a predefined pallette

- I could not find out how to define my own new color palette like
"white_red".
- Is there a way to "visualize" the color palettes before applying it to an
object?

Thanks for any help.

alex



>  Dr. Alexander Pautsch
>  Protein Crystallography /Structural Research
>  Boehringer Ingelheim Pharma GmbH & Co. KG Deutschland
>  Birkendorferstrasse 65
>  88400 BIBERACH, Germany
>  tel. +49 - (0)7351 - 54 4683
>  fax. +49 - (0)7351 - 83 4683
>  email alexander.pautsch@bc.boehringer-ingelheim.com
>
>
>