default msms_redirect.cpp Popular

msms_redirect.cpp : this file is used to allow full VMD visualization of the surface. This program redirects VMD to the two saved files triangulatedSurf.off.vert, triangulatedSurf.off.face. This redirect is used because VMD is not able to enable all surface visualization features when a saved file is loaded; that is a specific VMD program path has to be used. If you load an MSMS external file, surface effects cannot be applied. In order to get a proper visualization the following steps must be followed:

1) Compile msms_redirect, call it MSMS and put it into the VMD folder

2) Start VMD, load your pdb file and request for MSMS surface: this will generate the file atoms.xyzr

3) Feed atoms.xyzr to NanoShaper to get the desired mesh

4) Convert the .off file together with atoms.xyzr in MSMS format by off2msms.py.

5) Name the two files as triangulatedSurf.off.vert, triangulatedSurf.off.face, and copy them on VMD folder

6) Request again to VMD the MSMS surface. The surface computed by NanoShaper should be visualized.

At this last point VMD will run msms_redirect that will copy the two desired files triangulatedSurf.off.vert, triangulatedSurf.off.face into the temporary files that VMD 'believes' are from MSMS. At this stage you will get the raw surface together with proper atom info (if provided). It is up to the user to grant the consistency of the pdb loaded in VMD and the .xyzr file provided to the off2msms.py script.