Hi, I exported a PDB file from PyMOL that includes explicit water from a
dynamics track. However, many of the solvent molecules are either
doubled (same residue number for two different waters) or truncated
(missing a hydrogen, or a hydrogen given a separate residue number). I
am assuming th
Hi Tom,
There is the "connect_cutoff" setting, see
https://pymolwiki.org/index.php/connect_cutoff
The bonds do not affect residue numbers in PyMOL, those should be unchanged and
identical to your original input file.
Cheers,
Thomas
On 03 Jan 2017, at 07:07, Thomas Charles Pochapsky
wrote:
Hi Tom,
Do consider that
1. the PDB format only allows four digits for residue numbers, such that
water molecules must get the same number of there are more than of
them.
2. periodic boundary conditions may cause water molecules to be split,
making water molecules seem to miss an atom or hy
