pymol-users

[PyMOL] Installing DSSP/Stride plugin

[James S. <jms...@gm...>]

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 ] arg    Input file
  -o [ --output ] arg   Output file, use 'stdout' to output to screen
  -v [ --verbose ]      Verbose output
  --version             Print version
  -d [ --debug ] arg    Debug 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

PyMOL>run 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

Re: [PyMOL] Installing DSSP/Stride plugin

[lina <lin...@gm...>]

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 ] arg    Input file
>   -o [ --output ] arg   Output file, use 'stdout' to output to screen
>   -v [ --verbose ]      Verbose output
>   --version             Print version
>   -d [ --debug ] arg    Debug 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
> 
> PyMOL>run 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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