Hi Stephane,
you can select those waters using the within or gap selection
operators. within measures from the atom centre, whereas gap takes
the VDW radius into accout but selects everything beyond instead of
near. Have a look at those examples:
# use '... within ...'
select firstshell,
Thank you for your response, i will try your suggestion
A bientot
Stephane
De : Thomas Holder [ad...@thomas-holder.de] de la part de Thomas Holder
[spel...@users.sourceforge.net]
Date d'envoi : jeudi 22 septembre 2011 11:14
À : ABEL Stephane 175950
Cc :
On 12 sept. 2011, at 14:20, Jason Vertrees wrote:
Greetings,
One chance encounter at ACS couple weeks ago turned into a multi-day
discussion about using the new volume visualization for presenting
field data. Leroy Laverman from UCSB now has some example movies
showing how the
Hi Pymolers,
I need to perform a batch operation but I need a help with script
modification.
A have a set (~100) of pdb files that I would like to mutate all residues to
lysine. I modified mutate02.py script in pymol to perform this task, but I
would need two extra features:
1) the script would
Hi All,
With the help of Thomas Holder (thanks to him), now I can show and obtain
the number of water in the first shell of my six peptides (an amyloid
fibrils). However, I have a little problem with the command count_atoms in
my script
Below my script (*.pml) for Pymol 1.3 :
mstop
dss
hide
Thanks Marius
With the second it works
A bientot
Stephane
-Message d'origine-
De : Marius Retegan [mailto:marius.s.rete...@gmail.com]
Envoyé : jeudi 22 septembre 2011 18:02
À : intra\sa175950
Objet : Re: [PyMOL] Write in a file the number of water at a distance from a
Hello
# Firs load files in dirextory with:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
# load_sep.py
# Load multiple PDB files into a multiple PyMOL objects
# e.g. load_sep prot_*.pdb, prot
# will create objects with names, prot1, prot2, prot3, etc.
# Now the rest
cd /home/tlinnet/Desktop
#
And to save it, add this python block
python
for PDB in PDBs:
cmd.save(%s-K.pdb%PDB,%s%PDB)
python end
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/9/22 Troels Emtekær Linnet tlin...@gmail.com
# Firs
hi all,
I am writing this email with regards to the following problem.
Statement of the problem:
I have around 19,200 unique PDB files. Each of them have one or more ligands in
it.
For each ligand, I have to extract a zone which contains complete residues
within 4.5Angstroms of the ligand [ i.e.
