Dear Paul,
On 27.10.22 17:35, Paul Emsley wrote:
On 27/10/2022 08:53, Dirk Kostrewa wrote:
Dear Paul,
I would like to display local symmetry copies of my protomer molecule
during model building, in a similar way how it is possible for
displaying crystallographic symmetry copies. The local symmetry
operators could be provided for coot, say, by MTRIXn PDB records in
the general case, or by the local point group in the case of cryo-EM
(using RELION's symmetry conventions). After the local symmetry copies
have been generated, it would also be very useful if they could be
saved like crystallographic symmetry copies.
I think, displaying and saving local symmetry copies would be great
both for building models in crystallography using NCS, and in cryo-EM
using strict local symmetry.
What do you think about this?
An excellent idea, I think. So excellent that I implemented it and
released it in 0.9.6.
this is great ;-) !
Here's the API:
void add_molecular_symmetry(int imol,
double r_00, double r_01, double r_02,
double r_10, double r_11, double r_12,
double r_20, double r_21, double r_22,
double about_origin_x,
double about_origin_y,
double about_origin_z);
int add_molecular_symmetry_from_mtrix_from_file(int imol, const
std::string &file_name);
int add_molecular_symmetry_from_mtrix_from_self_file(int imol);
In the attached figure, I am building the chain at middle 10 o'clock,
the other chains are appearing (dynamically updating) because I
specified the molecular symmetry.
this is exactly what I imagined!
Paul.
Is there a way to use it from the coot GUI (maybe I have overlooked this)?
I found the commands "add_molecular_symmetry",
"add_molecular_symmetry_from_mtrix" and
"add_molecular_symmetry_from_mtrix_from_self_file" in Calculate ->
Scripting -> Python. Are these commands documented somewhere? I could
not find the equivalent Scheme commands in the Coot Online Manual.
Am I right that the copies generated by adding local symmetry operators
are separate molecules that can be easily saved?
Are you also planning to add local symmetry for cryo-EM structures by
providing the point group, maybe using RELION's symmetry convention?
Best regards,
Dirk.
--
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Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76998
E-mail: [email protected]
[email protected]
WWW: www.genzentrum.lmu.de
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