Re: [ccp4bb]: NCS solvents, per-residue analysis plots

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

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> -solvent atoms that can be matched in NCS pairs (again with a certain
> distance cutoff)

there's a WAters command in LSQMAN that does that;
see: http://xray.bmc.uu.se/usf/lsqman_man.html#S65

it will list matched solvent molecules and produce
a scatter plot file of delta-B versus distance
(e.g.: http://xray.bmc.uu.se/usf/pics/waters_1cel.gif)

> Also, I would like to prepare a publication quality plot of per-residue
> average B-factor vs residue number but do not have access to What-If. Is
> there another way of accomplishing this?

the BFactor PLot command in MOLEMAN2 does that;
see: http://xray.bmc.uu.se/usf/moleman2_man.html#S51

it produces a plot file which can be converted
with O2D to PostScript (for an example, see:
http://xray.bmc.uu.se/usf/pics/bf_av.gif) and
edited. alternatively, it can produce what it
calls a 'cricketgraph' file, which is simply
a tab-delimited ASCII file. this can be read
into just about any graphing and spreadsheet
program (not into BeebCalc on the ZX-81, though ;-)

--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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