Hello,
I've been working through different tabs of the AD plugin, trying to find
out what works with PyMOL v.1.7.1.3. The radio buttons on the grid tab are
not working, but the biggest hurdle I've come against to this point is on
the receptor tab. The plugin will correctly import the receptor file
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Hi I-Ji -
You say the superimposed atoms are still there; that seems like normal behavior
to me. If you disable one of the objects, can you see the other one, and vice
versa?
If the two structures are nearly identical, you may not be able to
differentiate them visually after alignment. If th
Hi,
And you can use get_raw_distances script at
http://www.pymolwiki.org/index.php/Get_raw_distances
to get detailed information about contacts.
Best regards,
Takanori Nakane
On 2014-05-27 15:24, Sampson, Jared wrote:
> Hi Merlin -
>
> Try limiting the distances shown to those between atoms in
Dear Thomas,
Thank you very much for your investigation.
I agree with you. PyMOL is doing right;
SCALEn should be the identity matrix, or CRYST1 expanded.
CRYST1 is defined to be "1 1 1 90 90 90" for
structures determined by non-crystallographic methods.
Thanks to the increased resolution of cry
Hi Merlin -
Try limiting the distances shown to those between atoms in specific selections
using the `distance` command. For example, to show H-bonds to solvent, disable
the “my_obj_pol_conts” object created by the technical preset and use the
command:
distance my_dist, my_obj and not solvent
Hi Takanori,
PyMOL uses SCALEn to transform into fractional coordinates, and then the
unit cell parameters (CRYST1) to transform back into cartesian
coordinates. The PDB spec says: "The unit cell parameters are used to
calculate SCALE". For 1VW3, CRYST1 defines a unit cube, so I assume
SCALEn shou
Dear PyMol users! I'm analysing polar contacts by "preset:technical". I got so
many yellow bar measurements that I can't count the number. IS there any else
way to count the number of all polar contacts ? Thanks for help, Merlin
