Hi Robert That seems like a great suggestion! I will give it a shot and let CCP4BB know if it works
Thanks Gina -----Original Message----- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Robert Campbell Sent: Wednesday, March 31, 2010 4:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] B factor Coloring in Pymol Hi Gina, On Wed, 31 Mar 2010 15:00:34 -0400 "Clayton, Gina Martyn" <gina_clay...@merck.com> wrote: > I am trying to colour a structure by B factor in Pymol. More > specifically I am colouring conserved residues (value in b factor). I > want to use 4 colours - say white, yellow, orange, red. However it > seems that Pymol now only allows 3 colours to be used - I tried the > script from the Wiki site, but Pymol will not accept the 4 rgb colours. > Does anyone have an idea how I can colour with 4 colours (but not > rainbow too confusing). Say, your b-factor values range from 0-10, and your object is called "protein", then you could do: color white, protein color yellow, protein & b > 2.5 color orange, protein & b > 5.0 color red, protein & b > 7.5 If you want to automate that process, then you need to write a script that determines, the b-factor limits for the 4 colours based on the b-factors present in your structure. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
