3v Volume Viewing Guide

Volume Viewing Guide

UCSF Chimera Tutorial

UCSF Chimera website provides a nice tutorial on using its program:

To view volume from the 3v website:

  • Download the gzipped MRC files
  • Download the gzipped PDB file
  • Unzip the MRC file, Chimera can read zipped PDB files, but not zipped MRC files
  • Open the files in Chimera
  • The a large window with the structure and the Volume Viewer window will appear
  • The MRC files generated by 3v are binary (values of 0 and 1)
  • The best threshold for 3v files seems to be 0.01
  • It is also a good idea to give the volume some color by clicking on the gray box
  • By selecting 'Surface and Mesh Options' from the Features menu you can add surface smoothing
  • With a little bit of playing you get an image like this

'3V: cavity, channel and cleft volume calculator and extractor' (free text)
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W555–W562
by Neil R. Voss and Mark Gerstein
Download source code
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If you find this useful or want more functionality please contact Neil <vossman77 [at] gmail [dot] com>
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