[Chimera-users] Modeling with cryo-EM

[Aurore Vaitinadapoule]

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

aurore <a.vaitinadapoule at inserm.fr>.vaitinadapoule at inserm.fr<a.vaitinadapoule at inserm.fr>
a.vaitinadapoule at gmail.com

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

Mobile phone: +33(0) 778 18 52 07
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