Nathan,
Strictly speaking, the issue may be with PDB2PQR itself, not APBS.
Furthermore, we don't yet know whether a combined development version of all
three packages would still reproduce the problem.
As an aside, a good reason for PyMOL to see PQR files is for diagnostic
visualization: to enab
Hi Warren --
The PQR format (which doesn't really have a standard) is basically
just whitespace delimited. I'm curious, though -- why would a PyMOL
APBS invocation ever see the PDB file? Wouldn't a user first convert
it to PQR with PDB2PQR (ideally) or with PyMOL's built-in functionality?
Joachim,
The trick with that is the same as in real life: you must place the camera
the same distance from each object you intend to photograph. But how can we
do this with PyMOL?
Ah ha! I've got it
The "center" command positions and points the camera at the molecule.
center object-name
And
Hi,
I noticed the latest version of the PDB file format description was
posted today.
http://www.wwpdb.org/docs.html
Chris
On 17 Sep 2008, at 20:21, DeLano Scientific wrote:
The PyMOL and APBS programs have differing views as to whether PDB &
PQR
files are column-based or space-delimi
Gilles,
The PyMOL and APBS programs have differing views as to whether PDB & PQR
files are column-based or space-delimited, respectively. We must eventually
sort this out, because it causes continued grief for our users in common.
For now, however, the workaround is to make sure no B-factors exc
Hallo,
we want to create a set of pictures from different molecules but the
zoom value should all be the same.
ANd is there an easy way to zoom in or out by e.g. 5%?
--
Joachim
I have noticed a strange behaviour of the APBS module. I used it a lot
recently and it works perfectly for 95% of the structures I analyzed. I
usually fetch the pdb code, then remove waters, heteroatoms and so on. I
also noticed that in some cases, when the b factor is quite big (over
100) APBS
