This is a question about Modeller and appears to have nothing to do with Chimera. Tom On Dec 13, 2013, at 10:11 AM, Aurore Vaitinadapoule wrote:

Dear all,

I'm would like tu use this following script to model with cryo-EM:

from modeller import *

log.verbose() env = environ()

struct='./M60_9.pdb' map='new_map.mrc' resolution=10.2 box_size=48 # how to define the box size ?? apix=1.88 x=90; y=63; z=23 #origin steps=20

# 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='CENTER', number_of_steps=steps, angular_step_size=30., temperature=100., best_docked_models=1, translate_type='RANDOM', em_fit_output_file='modem.log')

But i got this error message: _modeller.ModellerError: read_mrc_h_E> Density map must be cubic, and of dimension em_map_size (48): actual dimensions (40, 40, 36)

What is exactly the box size? And how to define it?

Thank's

Aurore

-- Aurore G. VAÏTINADAPOULÉ

PhD Student in Bioinformatics INSERM UMR-S665, DSIMB Team, Dynamique des Structures et des Interactions des Macromolécules Biologiques

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