USF

Uppsala Software Factory Tutorial - Visualisation of planes

This page describes how to visualise least-squares planes with O and MOLEMAN2. The procedure is illustrated using the structure of cellobiohydrolase I (PDB entry 8CEL, a theoretical model of CBH I in complex with a cellulose nanomer). We will generate planes for each of the nine glucose units, to visualise how the cellulose chain twists its way through the tunnel.

1 - Prepare a little MOLEMAN2 macro

This macro will do the work for one residue at a time. It asks which (glucose) residue number you want to generate a plane for, and the name of the output ODL file. It could loook like this:

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
! plane.momac - MOLEMAN2 macro to draw a least-squares plane
! through a glucose residue; only uses the ring atoms to define
! the plane
!
! Gerard Kleywegt @ 990315
!
! Enter the number of the glucose residue :
& resnum
! Enter the ODL file name :
& odlfile
! Now select this residue's ring atoms
sel none
sel or residue GLC
sel num and residue_nr $resnum $resnum
sel butnot atom " O2 "
sel butnot atom " O3 "
sel butnot atom " O4 "
sel butnot atom " O6 "
sel butnot atom " C6 "
! Generate the ODL file for the least-squares plane
ono ls_plane $odlfile $resnum yellow 1.0
!
! All done !
!
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
   

As it is, the colour in which the plane will be drawn is hard-wired, as is the margin (1.0 A) around the atoms of the ring for which the plane will be drawn. You can change these values, or use MOLEMAN2 symbols and prompt the user for values (so you could have alternating colours for alternating sugars, etc.).

2 - Create the drawing instructions

This we do with MOLEMAN2. First read the molecule (8CEL), then execute the macro we have just written (above):

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
 MOLEMAN2 > read 8cel.pdb
 Command > (read 8cel.pdb) 
 Reading from file : (8cel.pdb) 
 in normal PDB format
 ignoring hydrogen atoms
 ==> Found file in GKPATH : (/nfs/pdb/full/8cel.pdb) 
 HEADER :     HYDROLASE                               21-NOV-97   8CEL
 TITLE  :     THEORETICAL MODEL OF CBH1 IN COMPLEX WITH A CELLULOSE
 TITLE  :    2 NANOMER
 KEYWDS :     HYDROLASE, CELLULOSE DEGRADATION, GLYCOSIDASE, GLYCOPROTEIN,
 KEYWDS :    2 GLYCOSYLATED PROTEIN
 EXPDTA :     THEORETICAL MODEL
 AUTHOR :     C.DIVNE,J.STAHLBERG,T.A.JONES

 [...]

 Nr of selected atoms : (       3645) 
 MOLEMAN2 > @plane.momac
 Command > (@plane.momac) 
 ... Opened macro file : (plane.momac) 
 ... On unit : (      61) 
 Command > (! plane.momac - MOLEMAN2 macro to draw a least-squares plane) 
 Command > (! through a glucose residue; only uses the ring atoms to 
  define) 
 Command > (! the plane) 
 Command > (!) 
 Command > (! Gerard Kleywegt @ 990315) 
 Command > (!) 
 Command > (! Enter the number of the glucose residue :) 
 Command > (& resnum) 
 Value for symbol RESNUM ? ( ) 452
 Symbol RESNUM : (452) 
 Command > (! Enter the ODL file name :) 
 Command > (& odlfile) 
 Value for symbol ODLFILE ? ( ) 452.odl
 Symbol ODLFILE : (452.odl) 
 Command > (! Now select this residue's ring atoms) 
 Command > (sel none) 
 Select NO atoms

 [...]

 Eigen value 1 =         12.4 Vector :  -0.756840 -0.408495  0.510220
 Eigen value 2 =          6.1 Vector :  -0.425544 -0.284535 -0.859041
 Eigen value 3 =          0.3 Vector :   0.496090 -0.867278  0.041515
 Determinant : (   1.000) 
 Eigenvector #3 defines the least-squares plane
 Equation:   0.496090 X +  -0.867278 Y +   0.041515 Z = -31.307896

 ATOM  3240  C1  GLC   452  Distance    0.323
 ATOM  3241  C2  GLC   452  Distance   -0.192
 ATOM  3242  C3  GLC   452  Distance    0.202
 ATOM  3243  C4  GLC   452  Distance   -0.249
 ATOM  3244  C5  GLC   452  Distance    0.212
 ATOM  3246  O1  GLC   452  Distance   -0.083
 ATOM  3250  O5  GLC   452  Distance   -0.212

 RMSD to plane : (   0.221) 
 Creating ODL file   : (452.odl) 
 Object name         : (452) 
 Object colour       : (yellow) 
 Border around atoms : (   1.000) 
 ODL file written
 Command > (!) 
 Command > (! All done !) 
 Command > (!) 
 ... End of macro file
 ... Control returned to terminal
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
   

Simply repeat the procedure for the other eight glucoses (residues 453 to 460), and you're done.

The individual ODL files will look like this:

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
! Created by MOLEMAN2 V. 960804/1.0.4 at Sun Aug 4 17:34:53 1996 for user gerard
begin pl1
  mode solid
  colour cyan
  poly 5
       10.82      47.99      64.71
       10.82      43.53      77.23
       22.76      53.15      77.23
       22.76      57.61      64.71
       10.82      47.99      64.71
  mode line
end_object
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
   

3 - Draw the planes in O

Start up O, and read your molecule (8CEL). Make a CA trace and draw the glucose nonamer. This may look as follows:

Picture

Now draw the nine least-squares planes:

      
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
draw 452.odl
 As3> O descriptor in computer file system
 As3> ODL command ignored: !
draw 453.odl
 As3> O descriptor in computer file system
 As3> ODL command ignored: !

[...]

dr 460.odl
 As3> O descriptor in computer file system
 As3> ODL command ignored: !
 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
   

And, hey-presto ! Here's one I prepared earlier:

Picture

Cute, huh ?


USF Latest update at 23 July, 2001.