Martin,
If you end up wanting to do this a lot then it might be worth looking
into Dangle ( http://kinemage.biochem.duke.edu/software/dangle.php ).
This is one of the tools from the Richardson Lab which allows quick
output of various bond length, angle, torsion and plane measurements.
-bob
On Fr
Hi Bondurant,
I really like the merging of the graphic beauty of pymol with the detailed
depictions of reduce and probe. I have a method that is a bit clunky for
doing what you ask, but I don't know if it ever made it to the mainstream
in MolProbity. The caveat of wanting to work with a ligand m
omeone would write a plug-in to integrate the Molprobity
> output in PyMol?
>
> I can definitely not do it, but maybe this could be an interesting feature
> request to the PyMol developers?
>
> All the best,
> Tim
>
>
>
> Am 30/08/14 01:53, schrieb Robert Immormino:
This series of commands seems to do the job although a little sloppy.
label alt a+"", "A%s-%s" % (resn, resi)
label alt b+"", "B%s-%s" % (resn, resi)
hide labels, alt ""
Cheers,
-bob
On 12/7/05, Seth Harris wrote:
>
> Hi,
>
> I'm writing a small script to visit alternate conformations, steppin
Chad,
You can try,
show spheres, resn HOH (or whatever your waters are called)
set sphere_scale, .2
set sphere_transparency, .5
Good luck,
-bob
On 3/20/06, Chad R. Simmons wrote:
> Hello,
>
> I am using "nb_spheres" to represent waters in a figure I am generating but
> cannot figure out how
Paul,
I'm actually quite interested in an answer to this question as well.
An example of what I have been able to do is this:
http://kinemage.biochem.duke.edu/~immormino/neca_new.png
I like using this type of rendering to look at a protein cavity from
inside the protein. For me it has been hel
Tina,
A work-around that does something like what you are looking for is:
load protein_with_alts.pdb, A
load protein_with_alts.pdb, B
hide everything,
show sticks, A and alt A
show sticks, B and alt B
set stick_ball, 1, B
set stick_overlap, -1.8, B
Cheers,
-bob
On 5/23/06, Nguyen, Tina (GSBS)
Ronald,
You can try the yale morph server:
http://molmovdb.mbb.yale.edu/molmovdb/morph/
There are probably other tools that will perform linear interpolation
of structures and output "intermeditate" .pdb files, which could be
cleaned up and used in pymol to create a similar, but more user
contr
Paul,
I think the reason the surface coloring "spills over" is because
there are some surface triangles that are shared by the selection you
want (red) and the neighboring residues (grey)... So it should work
if you only use one selection, by saying something like:
load my_protein.pdb,
show surf
Shivesh,
try
show ribbon,
set ribbon_sampling, 10
-bob
Kun,
When I'm interested in dimer interfaces, or protein ligand contacts I
usually use Molprobity to define the interface.
http://molprobity.biochem.duke.edu/
It is a bit of a process, but here's the rundown:
Load your .pdb into molprobity
Add hydrogens
Visualize interface contacts
Then select
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