Hi James and Greg,
On Oct 25, 2013, at 4:03 AM, Greg Landrum wrote:
1. Do I remember correctly that there was a proposal (from
Roger) to add some auto bond-type perception to the PDB parser for
ligands (or is that just wishful thinking!)?
Roger will have to confirm this, but I
Hi James,
Regarding the AssignBondOrdersFromTemplate() method:
As far as I understood, the PDB reader assigns bond orders to the amino
acids in a protein, but if a ligand is present it puts all bonds of it to
SINGLE bonds as auto bond-type perception is not trivial (see Roger's
comments).
Hi Sereina,
Sereina wrote:
Regarding the AssignBondOrdersFromTemplate() method:
As far as I understood, the PDB reader assigns bond orders to the amino acids
in a protein, but if a ligand is present it puts all bonds of it to SINGLE
bonds as auto bond-type perception is not trivial (see
On 25/10/13 08:09, James Davidson wrote:
Hi Roger,
Thanks for the response
The use of an integer file format flavor argument allows the caller to
customize the behavior of the readers and writers. The semantics is that a
reasonable default is zero (for all bits), but that new features may
Hi James,
Okay, now it's clear. I somehow (wrongly) thought the PDB reader would give
you the protein and the ligand as two molecules and then it wouldn't have
been a problem... I will discuss with Greg on how to best do this and get
back to you.
Best,
Sereina
2013/10/25 James Davidson
On Oct 25, 2013, at 10:11 AM, Roger Sayle wrote:
The use of an integer file format flavor argument allows the caller
to customize the behavior of the readers and writers. The semantics
is that a reasonable default is zero (for all bits), but that new
features may be added without changing
Hi James,
There's something very strange going on here with PyMol.
On Oct 25, 2013, at 1:09 PM, James Davidson wrote:
I can't see any double-bonds rendered in PyMOL:
CONECT344 10
Here atom 3 has two bonds to atom 4. Why isn't it displayed double?
This PDB *will* render
Hi Greg (et al.),
Thanks for the beta! I have been going through some of the recently-added
functionality, and had a couple of questions regarding the PDB reading /
writing.
1. Do I remember correctly that there was a proposal (from Roger) to add
some auto bond-type perception to the
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