6.5 Creating 2D Maps of the internal surface of a pore

A recent advance allows an alternative view of the internal surface of a pore - from the inside. In this case we set up a cylindrical co-ordinate system working from the pore centreline:

This coordinate system can then be used to display properties of the pore lining in two dimensions. A simple way of imagining how the maps are constructed is to imagine that the internal surface of the pore is cut down a line and then rolled flat. A number of properties of the internal surface of the pore can then be displayed, for instance, whether the surface is lined by oxygen or nitrogen atoms. An example of such a picture is given in the J. Mol. Graphics article which forms part of this documentation.

The change in the residues lining internal surface of phospholamban model structure during a molecular dynamics run (thanks to Mark Sansom for the coordinates). It is immediately apparent that the model is a 5 helix bundle and the changes to which residues line the pore are obvious. This picture was produced using surfer.

Such a map can be left monochrome or coloured according to residue properties. In this case a different colour is used for residues from different chains. Other possibilities are to colour residues according to residue number or charge.

How to produce 2D maps in practice

Because I know how hard up all you researchers are I have gone to the trouble of digging around for a free more machine independent solution. The best program which I found for the purpose was gnuplot

The first step is to do a hole run in which the 2DMAPS card is specified in the input file. In the ~/hole2/example directory the file "2dmap.inp" shows such an input file (directly adapted from "example.inp"):

! example input file run on Arseniev's gramicidin structure
! Adapted from standard example.inp to produce 2D maps see section 6.5
! of hole documentation for details.
coord  1grm_single.pdb          
radius ~/hole2/rad/simple.rad
cvect  0 1 0                    
cpoint 0 0 3             
sample 0.25                     
endrad 5.

shorto 2            ! cut down on output
2dmaps 2d_example   ! filename root - many files will be produced with
                    ! this as a start

The end of the output file (included as "2dmap.out") lists what has been produced:

2d_example_touch.grd for map of touching distance
2d_example_capost.dat for Calpha posting info
2d_example_caline.bln for Calpha connecting lines (blanking format)
2d_example_res.bln for contacting residue base map (blanking format)
2d_example_on_map.grd for map Oxygen/Nitrogen neighbour presence
  (value 1 for oxygen, -1 for nitrogen and zero for any other)
2d_example_resno_map.grd for map of residue number
2d_example_polar_map.grd for map of residue polarity
  (1 for glu,asp; -1 for lys/arg; +0.1 tyr,ser,his,gln)
2d_example_chain_map.grd for map of chain id
  (number is the offset ascii value for the character
   i.e. if chain id's go A, B, C numbers will go 1,2,3)
2d_example_for_make_post_map.hole for file to be used with make_post_map to make
 better post map
2d_example_resid.dat for residue patch identities
 HOLE: normal completion

Here is a more detailed description of what each file contains:

Files containing map type information:

fileroot_touch.grd

This contains information as to distance (in Angstroms) from the centre line to the closest atom surface at that point. Maps can display anisotropic features (such as side opening etc.).

fileroot_on_map.grd

This contains information as to whether the closest non-hydrogen atom to the HOLE surface at this coordinate is an oxygen (value +1), a nitrogen (-1) or something else. Used in the gramicidin map example

fileroot_resno_map.grd

This contains information as the residue number of the closest non-hydrogen atom to the HOLE surface at this coordinate (value is the residue number).

fileroot_chain_map.grd

This contains information as the chain identity of the closest non-hydrogen atom to the HOLE surface at this coordinate. Each chain with have a seperate numberical value starting at 1 and then equal to the ichar(chain_id)-ichar(chain_id_1st_atom)+1 (ichar() is fortran function giving the ascii number for any character). This map is used in picture of phospholamban above.

fileroot_polar_map.grd

This contains information as the polarity of the residue for the closest non-hydrogen atom to the HOLE surface at this coordinate. Value 1 for glu,asp; -1 for lys/arg; +0.1 tyr,ser,his,gln.

Files containing line drawing information:

fileroot_res.bln

This is not a map file but contains information as to the boundaries between different residues. Similar pictures can be gained by drawing maps with chain_id/residue number but the .bln file is neat and easy. In the phospholamban and the gramicidin pictures this is used to draw a black line between different residues in a neat way. This is one of the most useful files if you are limited to using gnuplot (see below).

fileroot_caline.bln

This file contains the information for drawing lines connecting the points of projection of Calpha atoms onto the surface. Very useful - shows the relation of the structure to the surface - see pictures of phospholamban above.

Files containing information for placing labels:

fileroot_resid.dat

This file contains the information for placing labels stating what residue each patch refers to. The label is placed at the centroid of the total positions for that residue. For complex maps in which a single residue has two or more patches this can mean that the label lies outside any of the patches involved. For this reason a way of producing better labels was written:

fileroot_for_make_post_map.hole

This file can be used with the seperate program make_post_map (supplied with hole and automatically setup with the package) to produce much better residue id labels than the ones above. To use simply get to the directory containing the file and type "make_post_map" (and the enter key) like in this example:

jura> cd ~/hole2/example
jura> ls *.hole
2d_example_for_make_post_map.hole
jura> make_post_map
 *** Program make_post_map ***
 
 Copyright 1997 by Oliver Smart and Birkbeck College
 Program modification number 0001 28-2-97
 HOLE release 2beta001 (28 Feb 1997)
 Program linked at Sat Mar  1 19:01:47 GMT 1997  
 Last modified .f files: 
          14 Mar  1 18:59 machine_dep.f -
       15933 Mar  1 18:59 vdwdot.f       
        2970 Mar  1 18:59 vdset.f        

 Please enter input hole format (old) filename
 defaults <2d_example_for_make_post_map.hole> ext:<.hole> (abort by EXIT or ^D) :  (hit enter key)
 Please enter output SURFER posting format (new) filename                   
 defaults <2d_example_for_make_post_map.dat> ext:<.dat> (abort by EXIT or ^D) :    (hit enter key)

 input file has info for    73 rows and   141 columns 
 Data limits X=   -180.000   180.000
 Data limits Y=    -17.500    17.500
STOP - make_post_map normal completion.
jura> 
	

In this case a file "2d_example_for_make_post_map.dat" has been produced. This contains sensible labels for each patch on the 2D map "occupied" by a different residue. The label is positioned at the point furthest from any other patch. The label list starts this the largest patch and goes to the smallest. If the map is rather cluttered simply delete the labels at the end of the file.

fileroot_capost.dat

This file contains labels for the positions of Calpha atoms projected onto the surface - useful in conjunction with fileroot_caline.bln which draws lines between the points.

Using gnuplot to draw maps

Gnuplot is a public domain quite reasonable 2D/3D graph plotter. It is command line driven and is supported on wide range of machines. The examples given here were run with gnuplot unix version 3.5 (pre 3.6) patchlevel beta 332 (run on a sg under IRIX5.2). For more details of gnuplot see the gnuplot homepage, a convenient European place to download the latest version of gnuplot is from this ftp site at the Department of Physics & Astronomy at the University of Southampton, UK.

In order to use the surfer type files with gnuplot then they must be converted into a form suitable for gnu. Conversion programs are supplied with HOLE and should have been setup automatically with hole. The following table describes how to convert each file produced by HOLE or make_post_map.

Note because gnuplot contour plotting allows only very limited features it may be best to concentrate on using the .bln and .dat type files in 2D mode (plot rather than splot).

Example application

The first thing to do is convert the files above into a suitable form:

jura> bln2gnu < 2d_example_caline.bln > 2d_example_caline.gnu
jura> bln2gnu < 2d_example_res.bln > 2d_example_res.gnu      
jura> make_post2gnu < 2d_example_for_make_post_map.dat > 2d_example_for_make_post_map.gnu
jura>

Then simply run gnuplot (!indicates a comment do not enter yourself!!)

jura> gnuplot

        G N U P L O T
        unix version 3.5 (pre 3.6)
        patchlevel beta 332
        last modified Sat Apr 12 06:39:51 BST 1997

        Copyright(C) 1986 - 1993, 1997
        Thomas Williams, Colin Kelley and many others

        Send comments and requests for help to info-gnuplot@dartmouth.edu
        Send bugs, suggestions and mods to bug-gnuplot@dartmouth.edu

Terminal type set to 'x11'
gnuplot> load "setup_gnu"  ! setup file - see below
gnuplot> load "2d_example_for_make_post_map.gnu" ! labels 
gnuplot> plot "2d_example_res.gnu" with l, "2d_example_caline.gnu" with l linewidth 6  ! plot both residue patch seperators and Ca lines  
gnuplot> set yrange [-17:17]  ! visual inspection of picture in Xwindow suggests need to reduce range 
gnuplot> replot ! yes that's better 
gnuplot> set output "2d_example_gnuplot.ps"
gnuplot> set term post ! output to postscript file 
Terminal type set to 'postscript'
Options are 'landscape noenhanced monochrome dashed defaultplex "Helvetica" 14'
gnuplot> replot
gnuplot> exit

The postscript file that results is included in the example directory and basically looks like this:

Map of the internal surface of Arseniev and co-workers structure for the channel form of gramicidin D. The surface is divided into seperate areas according to the residue of closest atom to the HOLE surface. The dotted line marks the projection that a line joining the alpha carbons of each residue makes in the coordinate space. The head to head dimer nature of the channel is immediately obvious.

# setup commands for using gnuplot with HOLE 
# to use type 
# gnuplot> load "setup_gnu"
# at the gnuplot> prompt 
# these are only a suggestion to get really pretty output you
# will probably have to modify them.
set parametric
set view 0, 0
set xtics -180, 90, 180
set noclabel
set nokey
set xlabel "angle from x-axis in degrees"
set ylabel "z coordinate in angstroms"
set cntrparam levels auto 30
set size square
# for splot do not want original data - only contours
# n.b. for plotting .bln (residue maps, calpha lines) use plot not splot
set nosurface
set contour

GOOD LUCK and let me know of any useful tips!

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