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 9999 of
them.
2. periodic boundary conditions may cause water molecules to be split,
making water molecules seem to miss an atom or hydrogen atoms appear alone.
3. The residue number is read from the PDB file as is, and if a hydrogen
atom gets a different number than the other two atoms from the same water
molecule, either the program used to generate the PDB file is at fault or
the file format is somehow broken.
Hope it helps,
Tsjerk
On Tue, Jan 3, 2017 at 2:35 PM, Thomas Holder <thomas.hol...@schrodinger.com
> wrote:
> 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 <pocha...@brandeis.edu>
> wrote:
>
> > 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 that PyMOL assigns bonds based on distance between atoms, is
> > there a way to minimize this? The RCSB doesn't like my current PDB file!
> >
> > Thanks, Tom Pochapsky
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
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