[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] problems with modem

Jochen Ismer wrote:
> 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:
> 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

Yes, there is a bug in the code - it uses only 2 digits for the starting
point, so won't work for starting points > 99. This will be fixed in the
next release, but for now you'll just have to use fewer than 100
starting points.

> Problem Number two is the Voxelsize. My map has Voxelsize 1.83 but the
> rusulting maps allways has Voxelsize 1 

I'm pretty sure the output maps should be generated using the same voxel
size as the input map. So it may be that the voxel size is not being
correctly written into the header of these maps. Are your output maps
also MRC?

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage