pymol-users

[PyMOL] Auto-launching in Mac Terminal

[Warren L. D. <wa...@de...>]

> I have a Mac TI powerbook running OSX.  Every time I launch a new
> terminal window, pymol launches.  For example, if I open 3 terminal
> windows, 3 pymol sessions also start.  How do I stop this?

What?  You don't want PyMOL to launch every possible opportunity?

Actually, I've encountered this problem myself -- very annoying...

What happened is that you saved the Terminal window settings while you
had a PyMOL session open, so OS X inferred that you were indicating a
desire to have PyMOL open as a default preference.

The only way I know of changing this is to text-edit
$HOME/Library/Preferences/com.apple.Terminal.plist and remove the
ExecutionString entry which contains PyMOL.  That means deleting those
two lines: the one which contains ExecutionString and the one with the
PyMOL launch command.

Sorry about this!

Cheers,
Warren

[PyMOL] Auto-launching in Mac Terminal

[William S. <wg...@ch...>]

> Actually, I've encountered this problem myself -- very annoying...
>
> What happened is that you saved the Terminal window settings while you
> had a PyMOL session open, so OS X inferred that you were indicating a
> desire to have PyMOL open as a default preference.
>
> The only way I know of changing this is to text-edit
> $HOME/Library/Preferences/com.apple.Terminal.plist and remove the
> ExecutionString entry which contains PyMOL.  That means deleting those
> two lines: the one which contains ExecutionString and the one with the
> PyMOL launch command.

The OS X Terminal.app allows you to customize various terminal windows 
by saving different sets of preferences.  What happens is that you 
somehow accidently saved the pymol-specific ones as your default.

Probably the simplest thing to do is

rm ~/Library/Preferences/com.apple.Terminal.plist

and either replace it with your carefully backed up copy, or else just 
re-set all the preferences next time you open terminal.

You can also avoid this problem by invoking pymol at the command line.  
For convenience,

alias pymol /Applications/PyMOL/Darwin/pymol.com

and then just type pymol next time you start it.  You can also open pdf 
files and/or .pml scripts in one command, eg:

alias pymol /Applications/PyMOL/Darwin/pymol.com -q 
/Users/username/pymol/alias.pml

Finally if you also are running the X-windows version, you may want to 
alias one of these to a different name (npymol or xpymol).

Bill

[PyMOL] Python commands and variables

[Shu-Hsien S. <sh...@bu...>]

Hi, 

I am new to Pymol with some experiences with Python.
I have a basic question which maybe a little stupid.
Does Pymal take Python commands in selecting atoms?
For instance:

i = range(1, 299)
select resi i

or, further:
for i in range(1, 299)
    select  resi i

I understand the above can be easily done with:
select resi 1-288

However, I am wondering if variables can work in Pymol in general.

Thanks!

RE: [PyMOL] Python commands and variables

[Warren L. D. <wa...@de...>]

Yes, but you need to write in Python directly.  For example:

from pymol import cmd
cmd.select("mysel","none")
for i in range(10,20): cmd.select("mysel","mysel or resi %d"%i)

Would work in a ".py" file.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Shu-Hsien Sheu
> Sent: Wednesday, August 27, 2003 1:10 PM
> To: pym...@li...
> Subject: [PyMOL] Python commands and variables
> 
> Hi,
> 
> I am new to Pymol with some experiences with Python.
> I have a basic question which maybe a little stupid.
> Does Pymal take Python commands in selecting atoms?
> For instance:
> 
> i = range(1, 299)
> select resi i
> 
> or, further:
> for i in range(1, 299)
>     select  resi i
> 
> I understand the above can be easily done with:
> select resi 1-288
> 
> However, I am wondering if variables can work in Pymol in general.
> 
> Thanks!
> 
> 
> 
> 
> 
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