Hi PyMOLers,
I have been tackling this problem (on and off) for quite some time now but
without any luck. I have been trying to create CGO triangles using the
following simple sample script:
###
from pymol.cgo import *
from math import *
from pymol import cmd
Hi Sean,
On Fri, 09 Jul 2010 11:05:09 -0400 Sean Law wrote:
> I have been tackling this problem (on and off) for quite some time now but
> without any luck. I have been trying to create CGO triangles using the
> following simple sample script:
>
>
> ###
>
> fr
Hello,
I am trying to run a simple python script from Pymol and cannot run it:
***
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain
# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z
obj =
Vivek,
you need to put the script in the directory from where you launched
pymol. I.e if you launched pymol from your home directory with pymol,
you need to place the script there.
Pymol knows some basic shell like commands, like cd, ls, and may be some
more. Using these should get you were you
On Fri, 09 Jul 2010 13:46:57 -0400 Vivek Ranjan wrote:
> Hello,
>
> I am trying to run a simple python script from Pymol and cannot run it:
> I saved the above in a file named "axes.py" and put it in the same
> directory from where I type "pymol" (on ubuntu linux). Then I type
> "run axes.py"
Hi gang,
Just wanted to share some notes on compiling and getting Pymol 1.3.x running
on OS X Snow Leopard. Before proceeding, you'll of course need the XCode SDK
which comes supplied with the OS X cd's or downloaded through apple's
developer site.
(1) Compilation:
For some reason, the included
Hi,
Your assumptions are correct, as I've copied and tested your code, which
works fine from the current working directory where I ran the pymol start
script. It's probably a quirk w/ your installation? Otherwise, you can just
specify the full path to your script or "cd" into the folder... either
Hello,
I downloaded a pymol script from
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ called
draw_cell.py. I have "Python 2.6.5", numpy version: 1.3.0, I
downloaded cctbx for unix (self extracting files) and installed cctbx
in my $HOME/bin/. I have also included the line (.
"/home/vranjan/
Hi gang,
Actually, I spoke too soon! I attempted this compilation to address another
user's problems with an external script. But as you can see from the
attachment, the main control window is not being rendered properly. Am
missing other libraries?
Thanks,
Paul
On Fri, Jul 9, 2010 at 12:53 PM,
Thanks for your mail. I did two things:
(i) typed the entire path starting from /home/../../draw_cell.py
(ii)"cd /home/../../" and then "run draw_cell.py.
It still gives me the same error of not finding cctbx. I checked if I
am in the correct directory by typing "pwd" and got the correct
answer.
On Fri, 09 Jul 2010 16:11:47 -0400 Vivek Ranjan wrote:
> Hello,
>
> I downloaded a pymol script from
> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ called
> draw_cell.py. I have "Python 2.6.5", numpy version: 1.3.0, I
> downloaded cctbx for unix (self extracting files) and installed cct
Did you try the macports (http://www.macports.org/) version?
Marius
On Fri, Jul 9, 2010 at 10:10 PM, Paul Rigor (uci) wrote:
> Hi gang,
>
> Actually, I spoke too soon! I attempted this compilation to address another
> user's problems with an external script. But as you can see from the
> attachme
Hi Marius,
So I grabbed Pymol through macports, but now the main control window isn't
being rendered. I also receive the following error message. I've truncated
the error message. I know that macports resolved the tk/tcl dependencies,
so I'm not sure what's up? Has anyone else run into this pro
This usually means that tk or tcl is not installed correctly.
You could try to google the error. This gives you an idea about the problem
99% of the cases. Also you can double check that everything is installed. $
port installed tk tcl pymol. On a macosx 10.5.8 I get:
pymol @1.3_0 (active)
tcl @8.5
Cool deal thanks.
I'll also need to make sure there's no clash between fink libraries and
macports. I know though that all of those macports libraries are active:
pymol @1.3_0 (active)
tcl @8.5.8_0 (active)
tk @8.5.8_0 (active)
I'll keep chugging away.
Thanks for your tips!
Paul
On Fri,
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