Hi,
I didn't include the XH bond distribution scripts with relax. There
were a couple of these to generate the figure. These 2 file have been
attached to this message. 'dist.py' generates parts c and d whereas
'dist_core.py' generates parts a and b. For those who are interested,
this figure is from my PhD thesis located at
http://eprints.infodiv.unimelb.edu.au/archive/00002799/. Note that the
file 'core' referred to in 'dist_core.py' is just a text file with one
residue number per line. Also, depending on how you look at these
scripts, be careful and maybe remove any line wrapping. I hope you find
this useful.
Regards,
Edward
On Mon, 2007-12-03 at 12:26 -0500, Douglas Kojetin wrote:
Hi Edward,
Is a relax script available that creates a PyMOL (or MOLMOL)
structure figure of the NH bond vector orientations, as shown in your
dissertation (Figure 7.8; page 252)?
Thanks,
Doug
# Script for creating a PDB representation of the distribution of XH bond
vectors.
# Create the run.
name = 'vectors'
run.create(name, 'mf')
# Load the PDB file.
structure.read_pdb(name, '../1F35_H.pdb')
# Select solely the XH vectors used in the analysis.
select.read(name, file='../rates.txt', change_all=1, column=1)
# Select solely the core residues which are already selected.
select.read(name, file='core', boolean='AND')
# Count the number of selected residues.
sel_count = 0
for i in xrange(len(self.relax.data.res[name])):
sel_count = sel_count + self.relax.data.res[name][i].select
print "Number of residues selected: %d\n\n\n\n\n" % sel_count
# Set the XH vectors.
structure.vectors(name)
# Create the PDB file.
structure.create_vector_dist(name, force=1)
# PyMOL.
pymol.view(name)
pymol.cartoon(name)
pymol.vector_dist(name)
# Script for creating a PDB representation of the distribution of XH bond
vectors.
# Create the run.
name = 'vectors'
run.create(name, 'mf')
# Load the PDB file.
structure.read_pdb(name, '../1F35_H.pdb')
# Select solely the XH vectors used in the analysis.
select.read(name, file='../rates.txt', change_all=1, column=1)
# Set the XH vectors.
structure.vectors(name)
# Create the PDB file.
structure.create_vector_dist(name, force=1)
# PyMOL.
pymol.view(name)
pymol.cartoon(name)
pymol.vector_dist(name)
My XH bond distribution scripts, Re: NH bond vector orientation figure in pymol/molmol