Re: [ccp4bb]: [ccp4bb] how to colour by radius?

[Gerard DVD Kleywegt <gerard@xray.bmc.uu.se>]

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> Could anyone give me ideas for how to colour cpk model atoms by radius from
> the centre of mass? I guess I could use multiple Molscript distance
> selections - but is there a program that would overwrite the B factor column
> with the radius? Then I could just colour by 'B factor'.

i have implemented this in moleman2 (http://xray.bmc.uu.se/usf). you'll need
to use the new BFactor PSeudo command (see
http://xray.bmc.uu.se/usf/moleman2_man.html#S57) with which you can replace
the B-values by a number of other properties, including the distance from the
centre-of-gravity (or any other point), the atomic convexity (A Pintar et al,
Bioinformatics 18, 980-984 (2002)), and Halle's predicted B-values (B Halle,
PNAS 99, 1274-1279 (2002)). there are also a number of other new commands that
make the process easier - BFactor SAve, BF REstore, BF SCale, and BF ODb; see
the manual

for an example (rasmol screendump) of a molecule colour-ramped by distance
from the protein's centre-of-gravity, see
http://xray.bmc.uu.se/gerard/junk/ramp.gif

--dvd

******************************************************************
                        Gerard J.  Kleywegt
    [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
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