Jorge
This somehow ended up in my spam. Can you send me the files off-list?
Cheers
Nigel
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Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : [email protected]
Web : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464
On Tue, Apr 16, 2024 at 11:33 AM Jorge Iulek
Hi,
Well, people are very busy, but maybe one starting information: is tightening of one single bond (through its sigma value) meant to be possible? Thanks!
Jorge
On 4/12/24 16:45, Jorge Iulek wrote:
Dear all,
I would like to change the sigma value for an already restrained bond. I enter for phenix.refine: " bond { action = add delete *change atom_selection_1 = chain D and resid 493 and name CA atom_selection_2 = chain D and resid 493 and name CB symmetry_operation = None distance_ideal = 1.532 sigma = 1.02e-2 slack = None limit = -1.0 top_out = False }
"
In the log I get:
" ... Custom bonds: bond: atom 1: "ATOM 14355 CA ALA D 493 .*. C " atom 2: "ATOM 14358 CB ALA D 493 .*. C " symmetry operation: x,y,z distance_model: 1.511 distance_ideal: 1.532 ideal - model: 0.021 slack: 0.000 delta_slack: 0.021 sigma: 0.0102 Total number of added/changed bonds: 1 ... "
But in the .geo file I read:
" User supplied restraints: 1 Sorted by residual: bond pdb=" CA ALA D 493 " pdb=" CB ALA D 493 " ideal model delta sigma weight residual 1.532 1.511 0.022 1.28e-02 6.10e+03 2.85e+00 " 1.28e-02 is the default value.
On the other hand, sigma changes for angles and dihedrals seem to work as expected (the intended values are echoed to the .geo file). To add up, if a bond is *added*, the value is in the .geo file.
I observe this for both 1.20.1-4487 1.21-5207 versions.
So, in short, should I be allowed to *change the sigma* for a specific *bond*? How should I do it? Thanks
Jorge
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