Hello,
Is there a way in Pymol to combine the trajectory with the camera
movement? I load the trajectory, which is a pdb file where each
conformation is represented as a model entry, and call pml script with
the view adjustment commands. If I call the following snippet, the
view is set to "YYY" th
Cool! It works!
(http://farm8.staticflickr.com/7241/7203500026_8c3755d704_s.jpg: water
at the picture do not fill the box along the z direction - that is
very bad)
>
> On Tue, May 15, 2012 at 6:31 PM, Tsjerk Wassenaar wrote:
>> Hi Boris,
>>
>> run lattice.py
>> create copy1,all
>> shift 1,0,0,co
Hi Boris,
run lattice.py
create copy1,all
shift 1,0,0,copy1
create copy2, copy1
shift 1,0,0,copy2
As a side note, don't trust your eyes too much when estimating
homogeneity. Humans are strongly inclined to see patterns, even if
they're not there. You probably want to calculate densities on a grid
Hi Boris,
> supercell.py almost fits to my needs: is there a way I can replicate
> the cell to look exactly the same - I don't want to change the
> coloring? I tried to call it with
> supercell 2,1,1, color=None
> but it doesn't help.
the color argument is for coloring the cell frame.
You can ju
Thanks to Tsjerk and Thomas
supercell.py almost fits to my needs: is there a way I can replicate
the cell to look exactly the same - I don't want to change the
coloring? I tried to call it with
supercell 2,1,1, color=None
but it doesn't help.
SuperSymPlugin12.py: can't make cctbx work: Oops! Supe
It works:
I have in ~/.pymol.rc:
# let's add the custom srctip repo dir:
sys.path.append(os.path.expanduser('~/.local/lib/python2.7/site-packages/pymol/scripts'))
# custom scripts:
import pmlrc
And here's a pmlrc.py (which I put in
~/.local/lib/python2.7/site-packages/pymol/scripts):
# code to b
Hi Boris,
you can make your own run command which searches a path:
python
import os
def run2(filename):
for p in ['', '/path/to']:
full = os.path.join(p, filename)
if os.path.exists(full):
cmd.do('run ' + full)
return
print ' Error: no such fi
That's the point - I can import from these directories - but can't
'run' from there.
I can only run a script by specifying the full path.
Boris.
On Tue, May 15, 2012 at 4:45 PM, Troels Emtekær Linnet
wrote:
> write this in pymol command window:
>
> import sys
> print sys.path
>
> There you can
write this in pymol command window:
import sys
print sys.path
There you can see where pymol is looking.
Or you can this to your .pymolrc in your home folder:
import sys
sys.path.append("/Path/to/your/Pymol-script/modules")
Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil:
Is there a way I can add a path to 'run' - so not to type the full
path to the script when I run it:
run /path/to/script.py
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security
Dear all,
I was playing with cealign in PyMOL and noticed the following discrepancy:
Results using cealign from PyMOL:
--- < snip > ---
...
PyMOL>load 1fsz.pdb
...
PyMOL>load 1tub.pdb
...
PyMOL>cealign (1fsz and chain A), (1tub and chain A)
RMSD 4.423531 over 272 residues
--- < snip > ---
vs. r
11 matches
Mail list logo
