Hi Tofayel
You can also use the zone feature in chimera : Volume viewer -> features -> zone
Then select the atoms around which you want to extract density (e.g. Select one whole individual protein model). Then click zone in the volume viewer. If you are happy about the result, you can click « Mask » and chimera will create a new volume containing only the density that you could see after clicking zone. This volume can be saved to a new mrc file.
You have to do it for each individual protein but if you have many proteins I guess you can automate that with chimera scripting.
Best
Benoit
Le 12.11.15 06:36, « Collaborative Computational Project in Electron cryo-Microscopy au nom de Tofayel Ahmed » <[log in to unmask] au nom de [log in to unmask]> a écrit :
>Hi everyone,
>
>From a cryo EM map of ribosome at 4.2 Ang resolution, what would be the most reliable way (generating least amount of artifacts) to isolate densities for individual proteins? After fitting the model in density, I have done following:
>
>1. chimera->volume viewer-> color zone->split map
>2. alternatively, I have used e2pdb2mrc.py to generate a density map from protein model, used 'vop resample #1 onGrid #2' to overlay/fit this density map onto original ribosome density, then used relion_mask_create to generate a gaussian mask (extended and soft-edged), and finally used 'e2proc3d.py --multfile' to multiply this mask with original ribosome density
>
>regards,
>Tofayel
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