Re: [ccp4bb]: protein alignment

[Gerard DVD Kleywegt <gerard@xray.bmc.uu.se>]

hi lesa,

i assume you mean CA-CA distances for aligned residues rather than per-residue
all-atom RMSD values ? if that is indeed the case, and if you have lsqman,
then try the attached macro ("align.lsqmac"). it will do an automatic
alignment, and will give you a list of CA-CA distances, a structure-based
sequence alignment, loads of statistics, and an O macro to draw the
superimposed structures together with a 'minimal soap surface'

--gerard

> Can someone point me to a program that will output a list of rmsd's 
> between two aligned structures by residue number?  My favorite alignment
> program is TOP, but it doesn't produce this info (or I haven't figured 
> out how to get it).  I also tried the ccp4 program "compar" but it 
> seems to only work if each protein has the same number (& type) of residues.  

******************************************************************
                        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
******************************************************************
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
******************************************************************

!
! align.lsqmac - Gerard Kleywegt @ 2001-11-22/2002-03-06,09-24,25
!
! LSQMAN macro with Gerard's favourite recipe for superimposing
! just about any two protein structures from scratch
!
! note: only works with LSQMAN version 9.3 or newer !
!
& pdb1 pdb1cbs.ent
! ==> PDB file of first structure ?
& pdb1
!
& chn1 a
! ==> chain to use in first structure (use _underscore_ for blank) ?
& chn1
!
& pdb2 pdb1pmp.ent
! ==> PDB file of second structure ?
& pdb2
!
& chn2 a
! ==> chain to use in second structure (use _underscore_ for blank) ?
& chn2
!
& omacfile q.omac
! ==> Name of output O macro file ?
& omacfile
!
& odlfile q.odl
! ==> Name of output ODL soap-film file ?
& odlfile
!
& vrmlfile q.wrl
! ==> Name of output VRML file ?
& vrmlfile
!
& pdbout1 q1.pdb
! ==> Name of output PDB file of first structure ?
& pdbout1
!
& pdbout2 q2.pdb
! ==> Name of output PDB file of second structure ?
& pdbout2
!
& logfile q.log
! ==> Name of log file with structure-based sequence alignment ?
& logfile
!
echo on
hetatm strip
hydrogen strip
set reset
nmr_mode first
chain_mode non-blank
!
! change the following line for nucleic acids !
atom_type ca
!
delete gmod1
read gmod1 $pdb1
!
delete gmod2
read gmod2 $pdb2
!
omacro init gmod1 $omacfile
!
set coarse
fast_force gmod1 $chn1 gmod2 $chn2 30 15 0.9
!
set intermediate
improve gmod1 $chn1 gmod2 $chn2
!
set reset
improve gmod1 $chn1 gmod2 $chn2
!
dp gmod1 $chn1 gmod2 $chn2 sq 3.5 10
omacro append gmod2
!
soap_film gmod1 $chn1 gmod2 $chn2 $odlfile
omacro write "!"
omacro write draw
omacro write $odlfile
omacro write "!"
omacro close
!
global gmod1 $chn1 gmod2 $chn2 3.5 $logfile
sh gmod1 gmod2
!
apply gmod1 gmod2
!
write gmod1 $pdbout1 $chn1
write gmod2 $pdbout2 $chn2
!
vrml init $vrmlfile
vrml add gmod1 $chn1 green
vrml add gmod2 $chn2 red
!
! ALL DONE !!!!
!