cluster coordinates to asymmetric unit
Hi, I'm trying to work out how to cluster atomic coordinates into one asymmetric unit in a crystal for a given spacegroup rather than the atomic coordinates placed in arbitrary asymmetric unit copies in the unit cell. I think the tools to be used must be in cctbx.crystal.direct_space_asu and I have been trying but failed to understand how the test tst_crystal_asu_clusters.py works. Is there already a phenix or cctbx program that can do this? Many thanks, Robert
Hi Rob, I don't know the most elegant way of doing this but this methods of xray.structure: def closest_distances(..) could probably serve as a source of solution ideas: if you know a coordinate inside ASU where you'd like to move your atoms from elsewhere, you could probably use embedded into that function class class map_next_to_model_and_find_closest_distances(..) Hope this helps to get started! Pavel On 11/7/24 10:39, [email protected] wrote:
Hi, I'm trying to work out how to cluster atomic coordinates into one asymmetric unit in a crystal for a given spacegroup rather than the atomic coordinates placed in arbitrary asymmetric unit copies in the unit cell. I think the tools to be used must be in cctbx.crystal.direct_space_asu and I have been trying but failed to understand how the test tst_crystal_asu_clusters.py works. Is there already a phenix or cctbx program that can do this?
Many thanks,
Robert _______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]
Thanks Pavel. I already solved this problem with code snatched from the sort_hetams program written by Nat Echols. But I'll try your suggestion as well. Rob On 05/12/2024 19:12, Pavel Afonine wrote:
Hi Rob,
I don't know the most elegant way of doing this but this methods of xray.structure:
def closest_distances(..)
could probably serve as a source of solution ideas: if you know a coordinate inside ASU where you'd like to move your atoms from elsewhere, you could probably use embedded into that function class
class map_next_to_model_and_find_closest_distances(..)
Hope this helps to get started!
Pavel
On 11/7/24 10:39, [email protected] wrote:
Hi, I'm trying to work out how to cluster atomic coordinates into one asymmetric unit in a crystal for a given spacegroup rather than the atomic coordinates placed in arbitrary asymmetric unit copies in the unit cell. I think the tools to be used must be in cctbx.crystal.direct_space_asu and I have been trying but failed to understand how the test tst_crystal_asu_clusters.py works. Is there already a phenix or cctbx program that can do this?
Many thanks,
Robert _______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]
-- Robert Oeffner 15 Bayford Place Cambridge, CB4 2UF Tel: +44 (0)7712 887 162
hello
On Thu, Dec 5, 2024, 8:16 PM Robert Oeffner
Thanks Pavel. I already solved this problem with code snatched from the sort_hetams program written by Nat Echols. But I'll try your suggestion as well.
Rob
On 05/12/2024 19:12, Pavel Afonine wrote:
Hi Rob,
I don't know the most elegant way of doing this but this methods of xray.structure:
def closest_distances(..)
could probably serve as a source of solution ideas: if you know a coordinate inside ASU where you'd like to move your atoms from elsewhere, you could probably use embedded into that function class
class map_next_to_model_and_find_closest_distances(..)
Hope this helps to get started!
Pavel
On 11/7/24 10:39, [email protected] wrote:
Hi, I'm trying to work out how to cluster atomic coordinates into one asymmetric unit in a crystal for a given spacegroup rather than the atomic coordinates placed in arbitrary asymmetric unit copies in the unit cell. I think the tools to be used must be in cctbx.crystal.direct_space_asu and I have been trying but failed to understand how the test tst_crystal_asu_clusters.py works. Is there already a phenix or cctbx program that can do this?
Many thanks,
Robert _______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]
-- Robert Oeffner 15 Bayford Place Cambridge, CB4 2UF Tel: +44 (0)7712 887 162
_______________________________________________ cctbxbb mailing list -- [email protected] To unsubscribe send an email to [email protected]
participants (4)
-
Pavel Afonine -
Robert Oeffner -
robert＠oeffner.net
-
Son Kenneth