Dear PyMOL list
I'm adding hydrogens to a crystal structure. Upon saving, however, I
realize all hydrogens have been added to the beginning of the PDB file.
Can PyMOL be configured such that the hydrogens are placed at the
intuitively appropriate place in the PDB file?
Thanks for any hints.
Hi Martin,
do you have retain_order set to 1? This is not the default. Try:
unset retain_order
save file.pdb
Cheers,
Thomas
Martin Hediger wrote, On 09/25/12 18:24:
Dear PyMOL list
I'm adding hydrogens to a crystal structure. Upon saving, however, I
realize all hydrogens have been added
Dear all, thanks for the feedback, I'll definitely give it a try.
On 16.03.11 16:50, Michael Lerner wrote:
I've had good results with MolProbity
(http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18ceventID=15
Dear All
I would like to ask if the PyMOL function to add hydrogens to an entire
protein also has options, meaning is it possible to set the protonation
state of individual residues specifically? Like in a list or something?
h_add, His202:+1 or so?
And, it can be relevant at what atom a residue
I've had good results with MolProbity (
http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18ceventID=15)
in the past.
I had a script that would let me cycle through all of the HIS residues, add
hydrogens, and cycle between states. It's broken at the moment. The
Hi all,
I'm trying to use PyMol to add hydrogen atoms to this small fragment of
a PDB file, the chromophore from the GFP structure 1EMA;
REMARK S65T Chromophore from Ormo's coordintes (1EMB).
HETATM 466 N1 CRO66 24.077 27.513 36.610 1.00
11.86 N
HETATM 467 CA1 CRO
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[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Buz Barstow
Sent: Wednesday, March 23, 2005 7:54 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Adding Hydrogens to GFP Chromophore
Hi
