Hi,
pdb2pqr.py doesn't exist in the pdb2pqr tar.gz file (for either 2.0.0 or
1.8 versions; in a previous question I was advised to use the 1.8
version) and consequently APBS tools doesn't work. I have tried turning
the pdb2pqr.py.in into pdb2pqr.py by removing the "in" extension, but
the APBS
Tsjerk and Ezra, thanks a lot for your thoughts.
Tsjerk I see your point that an assembly is one snapshot, and for many purposes
a single state object or multiple (grouped) objects will be desired. However,
loading the assembly into multiple states in the first place is not a dead end
and using
Hi Wenfu -
Cartoon putty representation varies the diameter of the putty tube based on the
B-factor column in the loaded PDB file. In your example file, all the
B-factors are 0.00. Perhaps you could use `cartoon tube` instead, which is
similar to putty, but uses a single cartoon_tube_radius s
Hi James -
Here is how I would label your objects in grid_mode:
# For each object, create a pseudoatom at its center of geometry to position
the label
pseudoatom myobj_label, myobj
# Set the label text for the pseudoatom
label myobj_label, "My Object"
# To show the label and the object in the
Hi pymol users,
I have a pdb file, which is from the result of a molecular dynamics simulation.
I want to present the structure with cartoon putty in pymol.
But I can only make it cartoon putty in Macpymol 0.99 version. When I use
pymol1.7 or 1.3 version, the error is like this: Extrude-Warning:
Hi James,
No, you can't set transparency based on b-factor.
As for the selections, don't use selection keywords (ss) as names.
Cheers,
Tsjerk
On Apr 12, 2015 3:25 PM, "James Starlight" wrote:
> and also a question-
> how it would be possible to do something with the selection based on
> the b
