Re: [PyMOL] default water bond lengths in PyMOL

[Tsjerk Wassenaar]

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 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  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 
> 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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Re: [PyMOL] default water bond lengths in PyMOL

[Thomas Holder]

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, 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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[PyMOL] default water bond lengths in PyMOL

[Thomas Charles Pochapsky]

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


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