[Chimera-users] Modeling with cryo-EM

Tom Goddard goddard at sonic.net
Fri Dec 13 11:27:46 PST 2013


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 
> 
> Mobile phone: +33(0) 778 18 52 07
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> Chimera-users at cgl.ucsf.edu
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