All the files used in this example are supplied with hole
and can be found in directory ~/hole2/example. If you
want to work through the steps involved then
use the files in ~/hole2/work as a starting point.
The starting point of the run is the structure
for the channel form of gramicidin A determined by Arseniev and co-workers
(A.S.Arseniev,I.L.Barsukov,V.F.Bystrov,A.L.Lomize, Yu.A.Ovchinnikov
1H-NMR Study Of Gramicidin A Transmembrane Ion Channel
Febs Letts. 186 168- 1985).
As the pdb file of this structure contains an ensemble of five
structures the first stage was to select out one of these with an
editor. The result is the file
1grm_single.pdb. Note
that if you wished to analyze all five structures at once this
would be possible by splitting the file into 5 seperate pdb
files and using a wildcard * in the coord
card.
This structure was then examined using QUANTA
- it is clear that the channel lies up the y axis. To
obtain an approximate starting point within the channel
two atoms were picked on opposite sides of the pore at the
centre and their coordinates were averaged (the result was 0. 0. 3.).
This information was then used to write a suitable hole control
file example.inp:
! This is an example of how to run hole
! example input file run on Arseniev's gramicidin structure
! note everything preceeded by a "!" is a comment and will be ignored by HOLE
!
! This example run by line:
! hole < example.inp > example.out &
!
! first cards which must be quoted
! note that HOLE is case insensitive (except file names)
coord 1grm_single.pdb ! Co-ordinates in pdb format
radius ~/hole2/rad/simple.rad ! Use simple AMBER vdw radii
! n.b. can use ~ in hole
cvect 0 1 0 ! channel runs approx up Y axis
cpoint 0 0 3 ! a point in pore
!
! now optional cards
sample 0.25 ! distance between planes
pltout example.qpt ! quanta plot file output
sphpdb example.sph ! pdb format output of hole sphere centre
! (for use in sphqpt program)
endrad 5. ! to avoid having enormous ends
molqpt stick.qpt ! qpt file of the molecule
! (stick plot in one colour)
hole is run by typing the command:hole < example.inp > example.out &Four files are produced at the end of the run (which should take less than five minutes on all but the slowest workstation):
We will use the program sphqpt to
produce a grid surface of the HOLE run colour coded according
to pore radius. Typed input is indicated jura>At the end of this we have produced a gridded hole surface in file example_grid.qpt. It is coloured so that parts of the channel whose pore radius is below 1.15 Å - which is the minimum radius to accommodate a water molecule - should be shown in red. Where the pore radius is above 2.3 Å - sufficient to fit two water molecules in side by side are going to be shown in blue. The intermediate zone with a pore radius sufficient to fit just one water molecule will be displayed in green.sphqpt® *** Program sphqpt *** Reads a pdb format file produced by hole option SPHPDB which contains sphere centre info, and outputs a quanta plot file with the hole surface either as a dot or grid representation Version H2alpha1 (c) 1996 Oliver Smart & Birkbeck College, All rights reserved. Program linked at Mon Feb 26 16:24:34 GMT 1996 Last modified .f files: 24389 Feb 26 16:22 machine_dep.f 26903 Feb 26 16:21 sphqpt.f 10593 Feb 26 16:21 qplot.f Please enter input pdb format (old) filename defaults <example.sph> ext:<.sph> (abort by EXIT or ^D) :® # the default name is correct just hit return Please enter output binary hydra/quanta plot (new) filename defaults <example.qpt> ext:<.qpt> (abort by EXIT or ^D) :example_grid® # new name Do you want the centre lines drawn in output file? (y/n) <y>:® # (yes) It is possible to enter a number to which all the sphere centre radii will be set regardless of value in file. Enter value <leave radii alone>:® # use default This program can either do a dot surface (which is fast) or a curving grid surface (which is must slower). Do you want a dot (D) or grid (G) surface? <dot>:g® # enter g for grid The density of the grid surface is controlled by DMULT A value of 2.0 will produce a rather rough surface, 1.3 a rather dense surface - 1.8 is a reasonable compromise. N.b. procedure takes much longer than dot surface. What value for DMULT? <1.8>:® # use default Do you want to colour surface according to pore radius? <n>:y® # colour according to radius What upper radius for low radius colour (red) <1.15>:® # use default What upper radius for mid radius colour (green) <2.30>:® # use default What upper radius for high radius colour (blue) <999>:® # use default Outputing centre line to quanta colour 4 (default yellow) Outputing low rad surface to quanta colour 3 (default red) Pass 1 for this colour Number of vertices output so far 0 Pass 2 for this colour Number of vertices output so far 0 Outputing mid rad surface to quanta colour 7 (default green) Pass 1 for this colour Number of vertices output so far 70 Pass 2 for this colour Number of vertices output so far 78 Outputing high rad surface to quanta colour 2 (default blue) Pass 1 for this colour Number of vertices output so far 81 Pass 2 for this colour Number of vertices output so far 81 STOP FORTRAN STOP - sphqpt normal completion. statement executed jura>
For information about getting you molecular graphics
program to display the file example_grid.qpt (produced in the previous step)
in conjuction with your molecule, see 6.2 Using molecular graphics:
with: quanta,
sybyl,
O,
mage,
insightII.The files:
We will now use the files example_grid.qpt
and stick.qpt with the program qplot to
produce a colour postscript picture.
jura>This results in a file colour.ps which I have converted to a gif using xpsview, snapshot and xv on a Silicon Graphics:qplot® This is program qplot which reads hydra/quanta plot files and produces postscript output Version H2alpha1 (c) 1996 Oliver Smart & Birkbeck College, All rights reserved. Program linked at Mon Feb 26 16:27:28 GMT 1996 Last modified .f files: 10587 Feb 26 16:27 qplot.f 24389 Feb 26 16:22 machine_dep.f 26903 Feb 26 16:21 sphqpt.f What level of questions/options do you want to be used? Options:- expert (E) or normal <normal>:® # use default Please enter input binary hydra/quanta plot (old) filename defaults <example_grid.qpt> ext:<.qpt> (abort by EXIT or ^D) : Have read a total of 2095 records so far Do you want to read another input file? (y/n) <n>:y® # want 2nd file Please enter input next binary hydra/quanta plot (old) filename defaults <input.qpt> ext:<.qpt> (abort by EXIT or ^D) :stick.qpt® Have read a total of 2667 records so far Do you want to read another input file? (y/n) <n>:® # use default Please enter output postscript file (new) filename defaults <stick.ps> ext:<.ps> (abort by EXIT or ^D) :colour® # outpt file colour.ps Do you wish to change the view with a rotation? (y/n) <no>:® # use default Do you want colour postscript output? (y/n) <n>:y® Do you want a black or white background? (b/w) <w>:® # use default Can either preserve default quanta colours or map all non-HOLE objects to cyan? Preserve quanta colours(P) or map to magenta? <map>:® # use default Do you want a Normal or Stereo picture? (n/s) <normal>:s® # want stereo STOP FORTRAN STOP qplot normal successful completion. statement executed jura>
