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One of the more useful ways to visualize the results of HOLE is to plot a graph (all those school teachers/university demonstrators must have some influence). Raw data which can be used for this purpose is written at the end of the text output file. This can be read into your favourite graph plotting program (I use sigmaplot). Clearly the pore radius determined should be placed on the y axis. For the x-axis you can either use the distance moved along the pore centre-line from the initial point (the first column of the data) or the x, y or z co-ordinates of the sphere centre (if the pore lies approximately in one of these directions). The former representation gives an indication of the straightness of the pore but comparison between runs is made more difficult by side to side jumps in the centre line. The latter representation, which was suggested by Mark Samson, is probably preferable as it allows easy comparison between the results of different runs and for the position of important atoms/residues to be marked on the graph.
The QUANTA 3D binary file .qpt can be displayed using QUANTA (or if you
have ancient E & S ps300's its predecessor HYDRA). The procedure for
this is first to import the pdb file of your channel into the QUANTA
(so that you can see it). Then use your mouse to select the option
"Create objects" (under the heading draw). You are then confronted
with a "dialogue box" asking for what type of object: select "quanta
plot file" and a name for the object. The molecule and the hole
through will then be displayed in conjunction.
You may find that the dots of the dot surface do not show up very
well in QUANTA. If this is the case you can use program
qpt_conv (see section 7.1) to
convert the dots to small crosses (a new .qpt file is produced).
The .qpt file must then be converted into a form suitable for
use with sybyl. Use program
qpt_conv
(with the option "S") to produce .plt2 file.
To use this file within sybyl simply display your
molecule without centering on input and then
at the Sybyl> prompt type:
You may find that the dots of the dot surface do not show up very
well in QUANTA. If this is the case you can use program
qpt_conv (see section 7.1) to
convert the dots to small crosses (a new .qpt file is produced).
The first step is to produce a .qpt file of a HOLE run
using a PLTOUT card in hole,
or using the program sphqpt
with a .sph file produced by a
SPHPDB card in HOLE (the hole
surface can be produced as a grid and colour coded using this option.
The .qpt file must then be converted into a form suitable for
use with O. Use program
qpt_conv
(with the option "O") to produce a "draw_object" file
which I give the extension of .obo. This is how I got to display
the example molecule and the the converted output of sphqpt
(run in the ~/hole2/example directory):
You may find that the dots of the dot surface do not show up very
well in QUANTA. If this is the case you can use program
qpt_conv (see section 7.1) to
convert the dots to small crosses (a new .qpt file is produced).
The first step is to produce a .qpt file of a HOLE run
using a PLTOUT card in hole,
or using the program sphqpt
with a .sph file produced by a
SPHPDB card in HOLE (the hole
surface can be produced as a grid and colour coded using this option.
The .qpt file must then be converted into a form suitable for
use with mage. Use program
qpt_conv
(with the option "K") to produce .kin file.
This file will contain kinemage instructions for the HOLE
objects alone. To view the HOLE objects in conjunction
with the molecule then you should use an editor
to merge this file with the output of prekin (if you
are doing this under ms-windows then use write rather
than notepad as the editor as the files are large).
To get decent rotation rates one must reduce the number
of lines to be drawn on a screen - so either turn off
all HOLE objects when adjusting the view or make
sure you use a low dot density (set by a
DOTDEN card or in sphqpt).
Depending on the machine the lines drawn can be rather
thick - if this is the case try turning on the "thin line"
option in the "Options menu.
Note that mage can produce side by side stereo so if you
can see stereo directly then put this option on or otherwise
try to get a pair of mirror type stereo glasses.
If you have configured your web browser (if you have this problem
look at this
guide from Protein Science) to be able to view
kinemages the have a look at this (30kb)
example.
The .qpt file must then be converted into a form suitable for
use with InsightII. Use program
qpt_conv
with the option "I". Unfortunately I no longer
have access to a copy of the program so the conversion program
is unaltered from release 1 of HOLE - in which there was little
colour coding. Here are the notes from the previous release:
the routine writes out a Biosym Insight II
special user format file (.usr). This should allow display of the dot surface and lines produced by HOLE with InsightII.
There are some differences between the file formats. A single .usr file can contain only dots or lines - not both. Therefore
you must run the program twice to convert a typical .qpt file produced by HOLE. Also because the .usr file format for text
records essentially only allow one record per file I haven't bother to convert these. Also the control of colour is very
different between the two formats. A LINE .usr file does not have any facility for changing colour in the file - all records
from the .qpt file will therefore be displayed in a single colour. If you don't like this you will have to use an editor to split
up the files. The DOT .usr file allows the specification of a different colour for each dot (by a number between 0 an 360).
At present all dots are given the same colour which can be specified by the user. To display the dot surface (or line objects)
first read in your molecule (from pdb file or similar) and then use the option "get" under the menu "user" to specify the .usr
file produced by qpt_insight. The "Reference_object" option should be "on" to avoid the object being centred.
From an
extremely preliminary use it appears that InsightII suffers from much the same problem as QUANTA in that dots do not
show up as being very bright - so it may be worth using program
qpt_conv (see section 7.1) to
convert the dots to small crosses (a new .qpt file is produced).
If you want to use colour coding etc. then the subroutine qptins
will need updating - either does this yourself or e-mail me so that
I can do it and you can test it
Unfortunately rasmol does not have any way to import graphical objects
as distinct from atoms. A work around (suggested by Roger Sayle)
is to treat the objects as atoms in a pdb file and use "CONECT"
records to join them up. (Another annoying thing is that rasmol
will rework out bonds if there is not at least one bond per atom -
which means that each move draw has to be represented by 3 lines not
one!) There is yet a further complication -
you cannot just append the resulting "object pdb-file" to the end
of the molecule's pdb file as rasmol will then work out
a new bonding list based on distance (and a mess will result!).
At present the only way to see the molecule and hole object
is to use the MOLQPT card to produce a
stick plot of the molecule and concatinate the result with the
HOLE object .qpt (from HOLE or sphqpt). This can be converted into
a pseudo-pdb file for rasmol. Note one loses all atom information
on the molecule this way. It would be possible to be more smart
about this but it may not be necessary as new versions of
rasmol which can read more than one molecule in are being developed
which may avoid the problem. This example (run in ~/hole2/example)
shows how you can use it:
VRML is supported in two ways by HOLE. The first is an option
in qpt_conv (V) which is similar to those described above and
converts the simple 3D move/draws so that they can be used in VRML.
The second is the program sph2vrml
which allows the production
of solid spheres instead of dot surfaces, this was developed by
Xiaonan Wang, a student at Birkbeck. The program produces a pretty crude output at
present - great advances are expected from more sophisticated
approaches being introduce by another student Guy Coates.
(more to be added).
6.2 Using molecular graphics
Quanta
Sybyl 
Sybyl> take filename.plt2
This works with sybyl6.0. At Birkbeck with sybyl6.1 the program crashes
but this is a problem with the program as it occurs even with
plot file produce using sybyl! O
O > s_a_i
Sam> Name of input file: 1grm_single.pdb
Sam> O associated molecule name: gram
Sam> File type is PDB
Sam> Nothing marked for deletion, so no compression.
Sam> Space for 142656 atoms
Sam> Space for 10000 residues
Sam> Molecule GRAM contained 34 residues and 272 atoms
Sam> Centre of gravity updated for 1 34
O > mol
O > Current molecule has not been loaded.
Mol> Molecule code name []: gram
O > zone
Mol> Zone [all molecule]:
O > end
O > draw_object example_grid.obo
As3> O descriptor in computer file system
O >
mage 
InsightII
rasmol 
jura> cat example.qpt stick.qpt > example_and_stick.qpt
jura> qpt_conv
*** Program qpt_conv ***
Version H2alpha1
(c) 1996 Oliver Smart & Birkbeck College, All rights reserved.
Program linked at Wed Feb 26 13:33:59 GMT 1997
Last modified .f files:
8318 Feb 26 13:33 qptras.f
3726 Feb 24 11:45 qpt_conv.f
27622 Dec 5 14:15 hcapgr.f
This program converts a .qpt file (as produced by hole)
to something else.
Output options
'A' to/from ascii version of original .qpt (can then edit)
'C' A .qpt file in which dots are replaced by 3D crosses
'L' A .qpt file with long lines split into smaller sections
(useful for proper depth queueing in qplot)
'I' InsightII format
'R' Rasmol format
'S' Sybyl format
'K' to David C. Richardson's kinemage format
'O' for use with O program
'V' to Virtual Reality Markup Language
Enter conversion option character
to view the file you create start rasmol (assuming you have it on your path)
jura> rasmol example_and_stick_rasmol.pdb
RasMol Molecular Renderer
Roger Sayle, August 1995
Version 2.6
[24bit version]
Number of Groups .... 1
Number of Atoms ..... 5688
Number of Bonds ..... 5688
RasMol>
If you have setup the application type correctly in netscape you can
see the result by clicking this
link.
VRML - virtual reality
markup language
6.3 Colours used in HOLE
The graphical output of HOLE is in the form of a .qpt file - QUANTA
binary plot format. The format of the file is described in the
discussion for the PLTOUT card.
HOLE objects are divided as follows:
(links are provided to sections which give information how to produce/turn off each kind of object)
In general if you use a molecular graphics program other than quanta then the output of program qpt_conv should conform to these colours as much as possible.
Object Quanta Alternative Default Quanta Default qplot Colour # Colour # Colour colour output
Centre line 4 15 Yellow Thick yellow Normal pore surface 7 17 Bright Green Open Green Low radius surface 3 16 Red Open Red High radius surface 2 18 Light Blue Open deep blue Capsule vectors 8 19 Purple Thick Cyan Closest atom lines 10 20 Salmon Thick Grey Stick copy of molecule 5 - White White/Magenta