Reduce also has an option to remove hydrogens at the command line.
[phenix.]reduce -Trim model.pdb
Cheers
Nigel
---
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.go
Dear Mohammad,
You can use 'modify pdb' tool in phenix utilities and select remove hydrogen
option.
Also, if you are familiar with Vim editor in linux then there is easy command
(:g/ H/d).
Regards,
NIKHIL G BHARAMBE,
Ph.D Student,
Prof. K. Suguna's Lab
Molecular Biophysics Unit (MBU)
II
On 19/05/15 11:55, Mohammad Khan wrote:
Dear all,
I have added hydrogens on my molecule using the Refmac option in Coot.
I now want to remove them. I tried various syntax but they didn't
work. Is there a simple way to remove them from the pdb?
This will create a new molecule that is a copy of
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Mohammad,
you can use e.g. the CCP4 tool pdbset with its keyword 'EXCLUDE
HYDROGENS'. You could also repeat the refmac run but ask refmac not to
include the hydrogen atoms in the output PDB. This is the default and
available as option from the cc
Dear all,
I have added hydrogens on my molecule using the Refmac option in Coot.
I now want to remove them. I tried various syntax but they didn't
work. Is there a simple way to remove them from the pdb?
Moreover, if I do my refinemnets with hydrogens in it, will it affect
my results, other than
