Dear Esben,
Gromacs can create pqr files, but does it in a very bad way - the radii
information comes from a very limited set of atoms, and not directly from
the forcefield parameters. A colleague of mine, Antonio Baptista, has
written an awk script that can generate a proper pqr file from a gro
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| Message: 3
| From: "Warren L. DeLano"
| To:
| Date: Thu, 10 Jul 2003 12:40:23 -0700
| Subject: [PyMOL] New Map Formats Coming...
|
| PyMOLers,
|
| In response to user requests, I have added support for BRIX ("O" maps)
| and FLD (AVS Field) map for
| From: "Warren L. DeLano"
| To:
| Date: Thu, 10 Jul 2003 12:40:23 -0700
| Subject: [PyMOL] New Map Formats Coming...
|
| PyMOLers,
|
| In response to user requests, I have added support for BRIX ("O" maps)
| and FLD (AVS Field) map formats in the current development version.
| Are there any ot
I have a problem representing the contact surface between, e.g., a protein
and its ligand. The surface is displayed, but it is full of holes,
apparently at the points of contact. The script:
load protein.pdb, protein
load ligand.pdb, ligand
hide everything
show surface, (protein and (ligand arou
Hi All,
I have a couple of artistic questions:
1. Is there a way to have smoothed loops for only a portion of a structure?
I would like to show the details of one portion of my molecule, while
keeping the rest of the molecule as cartoonish and simplistic as possible.
The "smooth loops" toggle un
Joe,
Currently with PyMOL, you are selecting are atoms, not points on
the surface. Thus, you may need to increase the distance by 1-2 A or so
to get what you want. It's also possible that something else is going
on.
I would not expect to see whole at the points of contact, but
> 1. Is there a way to have smoothed loops for only a portion of a
> structure?
> I would like to show the details of one portion of my molecule, while
> keeping the rest of the molecule as cartoonish and simplistic as
possible.
> The "smooth loops" toggle under the cartoon menu changes the smooth
Hello all,
I am trying to write a script that will go through each residue in a
dimer interface and determine for each one how close it is to the
partner monomer.
I can interactively plot all the distances within a certain cutoff
using the handy:
distance chosen, residue_selected_on_first_ch
