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Re: [ccp4bb]: measure circumference
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> Ok, my dimer is not a perfect sphere. Let's say I want to wrap a rope
> around my protein in a certain orientation. What word should I use for that
> distance instead of circumference? And which program can measure that
> distance?
it's not the word, it's the definition of what you want to measure. a
circumference is defined for a 2D object, so you need to intersect a plane
with your protein, and then measure the circumference in that plane. there
are at least three parameters:
- how do you orient the plane w.r.t to your protein ? e.g.
do you align your protein with its inertia axes along X, Y,
and Z and then take the XY plane ? (and at which height
in Z ?)
- how do you define the extent of your protein ? is it just
the CA trace ? or the van der Waals volume of the entire
protein ? with or without a solvent probe ?
- how do you define circumference ? if you wrap a rope around
your protein, it will cut across indentations and invaginations
on the surface - technically, this would not be a circumference
anyway - i don't have a quick solution, but here's how i would do it, off the
top of my head (the example uses chain B of pdb entry 8FAB, plus a bunch of
USF programs, as well as a piece or rope, some pins, and one of those little
thingummabobs that you use to measure distances on road maps):
(1) orient your molecule, either by hand or by aligning the inertia
axes (e.g., with moleman2). also translate the molecule such
that either the centre-of-mass or the point through which you
want to take the plane lies at the origin. for instance, in moleman2:
MOLEMAN2 > read 8fab.pdb
MOLEMAN2 > select and chain B
MOLEMAN2 > xyz align_inert
MOLEMAN2 > write 8fab_ali.pdb pdb selected
(2) create a map-like description of your protein. the simplest way
of doing this is to create a mask by associating one given radius
to all atoms. for instance, in mama (using default cell, grid,
and masking radius):
MAMA > new pdb m1 8fab_ali.pdb
MAMA > write m1 8fab.mask
(3) use mapman to plot the plane that you are interested in, e.g.:
MAPMAN > extract m1 plane_0z.pl2 z 0
or:
MAPMAN > extr m1 plane_0x.pl2 x 0
or you could make 2D projections instead:
MAPMAN > 2d_project m1 projz.pl2 z -30 29
etc. - whatever you decided you were interested in at stage (1)
(4) convert the plot file(s) to postscript (using O2D and the o2dps
script from ftp://xray.bmc.uu.se/pub/gerard/omac/o2dps):
unix > o2dps '*pl2' 2d
(5) plot the postscript file(s) and measure the circumference. if you
want to use the 'rope definition', put poster pins at the 'extremes'
of the protein contour and wrap a piece of rope around it (i.e.,
such that if the rope is tight it doesn't intersect with the protein
anywhere - if it does, add another pin, etc.), and measure the length
of the rope. calculate the scale factor from the plot (the grid
spacing was 1 A and the cell was 100 A by 100 A by 100 A). if you
want to use the conventional definition of circumference, i would
use one of those devices you use to figure out distances on road
maps (they have a wheel that you roll over the map). again, figure
out the conversion factor from the plot and work out the answer
in A, and once again the famous Bob will be your uncle !
the first 4 steps take a minute or so - i haven't actually done step 5 - i'll
leave that as an exercise to the reader. alternatively, you could write a
program that does what you want, of course :-)
--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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