Hi Everybody,im trying to fit a Protein- Structure into a Cryo-Em-Map. It's
a large Map of a ribosome. I had the fololowing code:
from modeller import *
log.verbose()
env = environ()
struct='RPS25.pdb'
map='Head40s.mrc'
resolution=7.3
box_size=200
apix=1.83
x=0; y=0; z=0 #origin
steps=100
# Read in cryo-EM density map
den = density(env, file=map, em_density_format='MRC',
voxel_size=apix, resolution=resolution, em_map_size=box_size,
density_type='GAUSS', px=x,py=y,pz=z)
# Fit the PDB file into the map by MC simulated annealing
den.grid_search(em_density_format='MRC', num_structures=1,
em_pdb_name=struct, chains_num=[1],
start_type='ENTIRE', number_of_steps=steps,
angular_step_size=40., temperature=120.,
best_docked_models=1, translate_type='RANDOM',
em_fit_output_file='modem.log')
To search the Entire Map I chose ENTIRE as start type in the de.grid_search.
It works until starting point 99. Than I get the following Errormassage:
C:\Dokumente und
Einstellungen\Jochen\Desktop\Arbeit\modeller\FitRPS25>mod9v5 mo
dem_mc.py
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "modem_mc.py", line 25, in ?
em_fit_output_file='modem.log')
File "C:\Programme\Modeller9v5\modlib\modeller\density.py", line 61, in
grid_s
earch
em_pdb_name, chains_num)
IOError: openf______E> Cannot open file RPS2_init_**.pdb: Invalid argument
Any Idea how to solve that problem?
Problem Number two is the Voxelsize. My map has Voxelsize 1.83 but the
rusulting maps allways has Voxelsize 1
Thanks for your help
Jochen
