Hi,
I am trying to compute the RMS between a PDB file and a Gromacs
trajectory. I can see that align does things correctly when:
align trj, pdb1, mobile_state=1
i. e., when I align the first snapshot of the trajectory with the PDB
file. I also understand that PyMOL does compute the RMS along
Is there a way to mutate a cytosine to 5-methylcytosine in Pymol? Can it be
done using the GUI?
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Hi Rachel,
You can do it using the PyMOL built-in Builder
http://www.pymolwiki.org/index.php/Builder
Cheers,
Osvaldo.
On Tue, May 5, 2015 at 2:18 PM, Werther, Rachel A rwert...@fredhutch.org
wrote:
Is there a way to mutate a cytosine to 5-methylcytosine in Pymol? Can it
be done using the
Hi Albert,
Please pay attention to the difference between all-atom RMSD and RMSD after
outlier rejection.
http://pymolwiki.org/index.php/Align#RMSD
If your trj and pdb1 have identical topology and matching atom identifiers,
then you can also use cmd.rms().
http://pymolwiki.org/index.php/Rms
Hi Derek,
Before you load anything, do:
PyMOL set use_shaders, 0
You will still see the flickering issue, but PyMOL will not crash.
I'm not up-to-date with the situation in VMware, but in Parallels you have to
install the Parallels-Tools in the client OS to get usable graphics. So it's
Hi Al,
you would need to go through the Python API:
python
rms=cmd.align(mobCA,tarCA, quiet=0)
print rms
python end
rms contains a tuple with various parameters related to the superposition. The
first value in the tuple i.e. rms[0] should be the RMS value.
HTH
Carsten
Terribly useful Carsten!
I could easily do a loop and get the RMS along the trajectory:
k = []
for i in range(1,101): k.append(cmd.align(trj,pdb1,mobile_state=i))
for i in range(100): print k[i][0]
Cheers,
Albert
On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote:
Hi Al,
you
