Re: [PyMOL] loading PQR-format coordinates

[wtempel <wt...@gm...>]

Thomas,
how did you know? I removed the --whitespace switch, and get a meaningful
model displayed in PyMOL. Has the mmcif format been suggested to the
PDB2PQR developers?
Many thanks.
Wolfram

On Thu, Dec 7, 2017 at 3:01 AM, Thomas Holder <tho...@sc...
> wrote:

> Hi Wolfram,
>
> Do you run pdb2pqr with the --whitespace option? If yes, remove that and
> see if PyMOL is happy with the output.
>
> Some versions of PyMOL's APBS Tools plugin have the --whitespace option by
> default (first page, "pdb2pqr command line options") but it seems that this
> flag creates about as many problems as it solves. The correct solution
> would be to retire the PQR format and replace it with mmCIF, which is not a
> fixed column format.
>
> Cheers,
>   Thomas
>
> > On Dec 7, 2017, at 1:14 AM, wtempel <wt...@gm...> wrote:
> >
> > Hello,
> > loading a pqr (PDB2PQR version 2.1.1) file into pymol 1.7 … 1.9 garbles
> the model in some systematic way, whereas PDB2PQR version 1.8 output
> appears to be displayed correctly. After superficial inspection I concluded
> that in 2.1.1 output, columns from (and including) the atom number appear
> to be shifted to the right by one position. Indeed, when I apply
> > sed 's/^ATOM /ATOM/', the so modified 2.1.1 output appears to be
> displayed correctly in PyMOL. My question to those familiar with pqr models
> and the pymol source: is the sed hack safe as in that it would not distort
> any subsequently calculated APBS surfaces?
> > Best regards.
> > Wolfram Tempel
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>