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