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Compiling external programs from source code

VMD uses several external programs for various tasks, these include the STRIDE secondary structure prediction program, the SURF solvent accessible surface program, and various other optional external rendering programs. Before one can build a complete VMD distribution, these external programs must be successfully compiled and installed into the correct locations in the vmd/lib directories. If you already have binaries of Surf or Stride, you can just copy them into the appropriate directories.

Compiling STRIDE from source code

STRIDE is used by VMD to compute the secondary structure given the protein 3D coordinates. The appropriate STRIDE binary is included in the VMD binary distribution. To compile it yourself, see the web site at
http://www.embl-heidelberg.de/stride/stride_info.html for information on how to get the source and see ./lib/stride for information on how to use it with VMD. If you're unable to get the STRIDE source code from the original site, a copy is also available here: http://www.ks.uiuc.edu/Research/vmd/extsrcs/Stride_src.tar.Z

Change line 43 of stride.h from

   define MAX_AT_IN_RES             50

to

   define MAX_AT_IN_RES             75
because there are many structures with non-standard residues containing more than 50 atoms.

Change line 96 of stride.c from

   return(SUCCESS);
to

   return(0);
since a program should return 0 if everything ended correctly.

Compiling SURF from source code

SURF binaries are contained in the VMD distribution, with permission from the authors. The SURF source code is no longer made available at UNC, so we have placed a copy of the SURF source code archive here: http://www.ks.uiuc.edu/Research/vmd/extsrcs/surf.tar.Z

To get SURF working for VMD:

  1. uncompress and untar surf.tar.Z
  2. make depend This uses 'makedepend' which is one of the binaries that comes with X11. It might not be in your path (eg, /usr/openwin/bin for Solaris 2.5).
  3. make
  4. mv surf surf_$ARCH (for example: mv surf surf_IRIX5)

Id:
pg_extprogs.dox,v 1.3 2008/03/04 20:15:49 johns Exp


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