Hi,
Since my edu copy failed after I upgrade to yosemite. I have downloaded pymol
on my iMac 10.10.1 following the fink for 10.10 instructions on scottslab web:
http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Fink_for_10.10
After setting up fink, I ran sudo apt-get install pymol-py27. I am s
Hi Lau,
If you install from command line, it will most likely install to
/usr/local/bin/. The problem is, your icons probably link to the app you
uninstalled. I would try to find the /usr/local/bin/pymol in your finder
window, then drag the binary to your desktop in you want an icon. If you rea
(2) assuming you didn't change it when installing fink, fink will install
pymol in the /sw/bin directory.
(4) this is fink setting environment variables such as PATH. You can add a
line to your .bashrc to source it so it will be sourced every time you open
a terminal.
On Mon, Jan 19, 2015 at
Hi everyone,
On 19 Jan 2015, at 03:30, Jordan Willis wrote:
> [...] If you really want a fresh install I would delete all the pymol
> directories in your computer with a find command like, and run a fresh
> install...
>
> sudo cd / ; find . -name “*pymol*" -exec rm -rf {} \;
>
> However, tha
Hi Carsten,
This sounds like a non-trivial problem, my understanding is that it's still
an ongoing challenge to best align dissimilar structures. Other ways of
aligning structures involves using the vectors from secondary structure
elements, or feeding in (multiple) sequence alignments. All have t
Hi Carsten & Shane,
I assume Carsten is looking for cmd.get_raw_alignment(). Recent versions of
PyMOL can create an alignment object with all alignment commands (align, super,
cealign). get_raw_alignment returns the (model, index) keys for all pairs.
http://pymolwiki.org/index.php/get_raw_align
Yep, that was it and will take care of most of the issues I encountered. Just
stumbled upon colorbyrmsd.py, which contained that function a couple of minutes
ago as well.
Thanks for all the suggestions and pointers!
Cheers,
Carsten
-Original Message-
From: Thomas Holder [mail
