Re: [PyMOL] Mesh Cavity Mode?

2013-03-23 Thread Thomas Holder 
Hi Jared,

how about:

PyMOL as surface
PyMOL set surface_cavity_mode, 1
PyMOL set surface_type, 2

Cheers,
  Thomas

Sampson, Jared wrote, On 03/22/13 23:31:
 Hi all - 
 
 Is there a way to show internal cavities as meshes instead of surfaces?
  Something like `set surface_cavity_mode, 1` except with mesh?
 
 Thanks in advance for responses.
 
 Cheers,
 Jared

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

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Re: [PyMOL] Installing DSSP/Stride plugin

2013-03-23 Thread lina 
The way I did:

1] sudo pymol
PyMol --  Plugin -- Manage Plugins -- install
install the pymol_dssp_stride.py

2] restart pymol
Plugin-- DSSP  Stride


On Saturday 23,March,2013 11:46 PM, James Starlight wrote:
 Dear PyMOl users!
 
 I've forced with the problem during installing of the DSSP/STRIDE plugin.
 
 In particular I've download pymol's plugins (and installed it via the
 plugin's meny) as well as DSSP binaries.
 
 then I've add DSSP_bin to the bash.rc
 
 so in the terminal I can launch it
 
 own@starlight ~/Documents/pymol $ dssp
 DSSP 2.0.4 options:
   -h [ --help ] Display help message
   -i [ --input ] argInput file
   -o [ --output ] arg   Output file, use 'stdout' to output to screen
   -v [ --verbose ]  Verbose output
   --version Print version
   -d [ --debug ] argDebug level (for even more verbose output)
 
 
 Examples:
 
 To calculate the secondary structure for the file 1crn.pdb and
 write the result to a file called 1crn.dssp, you type:
 
   dssp.exe -i 1crn.pdb -o 1crn.dssp
 
 but I cant use it in the pymol window.
 
 When I've tried to launch pymol script manually
 e.g by run pymol_dssp_stride.py
 
 I've obtained alot of errors that dssp and stride have not been launched.
 
 If I tried to start pre-installed script by
 run dssp
 
 I've obtained
 
 PyMOLrun dssp
 Traceback (most recent call last):
   File /usr/lib/python2.7/dist-packages/pymol/parser.py, line 338, in parse
 parsing.run_file(path,self.pymol_names,self.pymol_names)
   File /usr/lib/python2.7/dist-packages/pymol/parsing.py, line 455,
 in run_file
 execfile(file,global_ns,local_ns)
   File dssp, line 1
 SyntaxError: Non-ASCII character '\xb7' in file dssp on line 2, but no
 encoding declared; see http://www.python.org/peps/pep-0263.html for
 details
 
 How Should I fix it?
 
 Thanks for help
 
 James
 
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