Hi All,
I am using Pymol to make figures for my publication. I am not sure if there has
been a discussion earlier but I would like to know how we can label the
secondary structures (helices and strands) using Pymol. I have them defined in
my header file using DSSP.
Thank you in advance.
Hi Bishwa,
can you be more precise what you mean by label? If the secondary
structure is defined in the header of your PDB file, PyMOL can show
cartoon representation, show text labels on C-alpha atoms and color by
secondary structure.
PyMOL as cartoon
PyMOL label name CA, ss
PyMOL color red, ss
Dear Thomas,
Even after I installed the Pmw1.3 which should be compatible with python2.7
and reinstalling the pymol, I am still the following error message.
File /Library/Python/2.7/site-packages/pymol/__init__.py, line 450, in
launch_gui
__import__(self.invocation.options.gui)
File
Dear Rhitankar,
I should point out that Schrödinger also sells pre-compiled PyMOL with
easy to use installers. http://pymol.org/academic.html
Open-Source PyMOL was always targeted to power-users who are familiar
with compiling software themselves.
Regarding your question: It will most likely
Dear Thomas,
Thanks for the informations. I think I am able to use port to install the
pymol1.5 version but I would also need to remove the existing 1.6 version.
Can you tell me the command to uninstall the existing version and then do a
fresh installation?
Thanks again
Rhitankar
On Wed,
Hi Rhitankar,
this depends which python you used and which arguments you passed to
setup.py. I assume you used system python and no arguments, then just
remove these:
/Library/Python/2.7/site-packages/pymol
/usr/local/bin/pymol
Cheers,
Thomas
Rhitankar Pal wrote, On 05/08/13 18:46:
Dear
Hi Bishwa,
what you want is to label one representative atom per secondary
structure element. So figure out chain and residue number of those
atoms, and label each of them individually:
PyMOL label A/42/CA, beta1
PyMOL label A/117/CA, alpha1
PyMOL label A/147/CA, alpha2
For changing label font,
