Hi,
I need to calculate the RMSD between two ligands (around 50 atoms). For
proteins works very well but it seems that for small molecules it gives
errors. I looked through the forum and I did not find any useful info. I
tried rms , rms_cur and so between the atoms selections but I get errors
I know in the past this question was to be addressed in a future version.
Anyway, after aligning two structures, is there a way to dump out the
sequence alignment (i.e., as a msf file) or is the alignment display
onscreen the only way to see it?
Evan Sadler
--
J. Evan Sadler, M.D., Ph.D.
Howard
Hi All,
I am using MacPyMOL 0.99rc6 on Mac OS X leopard (10.5.1). I wanted to
import the pymol modules into python. As suggested by
MacPyMOL.app/pymol/modules/pymol/__init__.py I set the following
environment variables:
export
PYMOL_PATH=$PYMOL_PATH:/Volumes/Home/shatadal/Programs/MacPyMOL.app/p
Horacio,
PyMOL cannot currently superimpose small molecules unless:
1. either the identifiers match between the two molecules (fit commmand)
or
2. the pairwise correspondance between the two is explicitly specified
(pair_fit command or pair fitting wizard)
Cheers,
Warren
--
DeLano Scientific
Evan,
You can save the "alignment" object resulting from an align command to an
aln file:
align sele1, sele2, object=aln_obj
save alignment.aln, aln_obj
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:del...@delsci.info
> -Original Message-
> From: pymol-u
Unfortunately, this cannot work since MacPyMOL embeds Python directly.
Your choices are as follows:
1. run your Python scripts from within MacPyMOL
2. launch PyMOL in command-line mode with your script
/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -qc script.py
or
3. compile the open-sou
Richard,
It is fair to say that scenes and mdo commands are effectively distinct
through the PyMOL 1.0x releases. One can either program movies manually
(via mdo, mview, scene, movie.rock, movie.roll, etc.), or one can deliver
presentations live from within PyMOL using scenes (stored in sessions)
Hi I have a running pymol session with nothing loaded. I now want to load a
cgo object into this session. When I read in the cgo file using either
command line (load /Users/hari/Desktop/test.cgo , test ) or the GUI menu ,
I get an object entry on the side panel but nothing shows up in the viewing
Hi All --
Yes, I know I want to do something silly here, but does anyone know of a
"jiffy" that will generate anisotropic thermal parameters for an
isotropic atom?
My end goal is to create a figure showing a ligand as ball-and-stick
where the spheres are scaled by the B-factor. Since I'm not d