change sigma for an already restrained bond
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
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
Jorge
This somehow ended up in my spam. Can you send me the files off-list?
Cheers
Nigel
---
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
phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
Hi Jorge, to answer your question and for the record, the following exercise: phenix.fetch_pdb 1yjp --mtz phenix.refine 1yjp.{pdb,mtz} output.prefix=1 params.eff write_final_geo_file=true > & 1.zlog & phenix.refine 1yjp.{pdb,mtz} output.prefix=2 params.eff write_final_geo_file=true cdl=false > & 2.zlog & confirms that you can override standard bond lengths and sigmas. In the first case I see (both geo files): User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 1.456 1.459 -0.003 1.21e-02 6.83e+03 4.30e-02 and User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 1.458 1.458 -0.000 1.19e-02 7.06e+03 2.44e-04 And in the second case I see User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 2.000 1.459 0.541 1.00e-02 1.00e+04 2.93e+03 and User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 2.000 1.987 0.013 1.00e-02 1.00e+04 1.79e+00 NOTE the nuance: you need to disable CDL for this to work as you want. Pavel On 4/16/24 11:23, Jorge Iulek wrote:
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
phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
Dear Pavel, Thank you; Nigel has also written me, I have tested according to your directions and it works. One has to setup up cld=False as you point (but this is not needed for angles, dihedrals). Sincerely, Jorge On 4/18/24 21:35, Pavel Afonine wrote:
Hi Jorge,
to answer your question and for the record, the following exercise:
phenix.fetch_pdb 1yjp --mtz phenix.refine 1yjp.{pdb,mtz} output.prefix=1 params.eff write_final_geo_file=true > & 1.zlog & phenix.refine 1yjp.{pdb,mtz} output.prefix=2 params.eff write_final_geo_file=true cdl=false > & 2.zlog &
confirms that you can override standard bond lengths and sigmas.
In the first case I see (both geo files):
User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 1.456 1.459 -0.003 1.21e-02 6.83e+03 4.30e-02
and
User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 1.458 1.458 -0.000 1.19e-02 7.06e+03 2.44e-04
And in the second case I see
User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 2.000 1.459 0.541 1.00e-02 1.00e+04 2.93e+03
and
User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 2.000 1.987 0.013 1.00e-02 1.00e+04 1.79e+00
NOTE the nuance: you need to disable CDL for this to work as you want.
Pavel
On 4/16/24 11:23, Jorge Iulek wrote:
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
phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
Hi Jorge, great you got an answer from Nigel. I have not seen any reply on the phenixbb list so I replied as well. OK, it sounds like the problem is solved! All the best! Pavel On 4/18/24 18:00, Jorge Iulek wrote:
Dear Pavel,
Thank you; Nigel has also written me, I have tested according to your directions and it works. One has to setup up cld=False as you point (but this is not needed for angles, dihedrals). Sincerely,
Jorge
On 4/18/24 21:35, Pavel Afonine wrote:
Hi Jorge,
to answer your question and for the record, the following exercise:
phenix.fetch_pdb 1yjp --mtz phenix.refine 1yjp.{pdb,mtz} output.prefix=1 params.eff write_final_geo_file=true > & 1.zlog & phenix.refine 1yjp.{pdb,mtz} output.prefix=2 params.eff write_final_geo_file=true cdl=false > & 2.zlog &
confirms that you can override standard bond lengths and sigmas.
In the first case I see (both geo files):
User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 1.456 1.459 -0.003 1.21e-02 6.83e+03 4.30e-02
and
User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 1.458 1.458 -0.000 1.19e-02 7.06e+03 2.44e-04
And in the second case I see
User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 2.000 1.459 0.541 1.00e-02 1.00e+04 2.93e+03
and
User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 2.000 1.987 0.013 1.00e-02 1.00e+04 1.79e+00
NOTE the nuance: you need to disable CDL for this to work as you want.
Pavel
On 4/16/24 11:23, Jorge Iulek wrote:
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
phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
According to my current tests, yes. Thanks. Just correcting my mistyping, one has to setup like you mention: cdl=False. J. On 4/18/24 22:09, Pavel Afonine wrote:
Hi Jorge,
great you got an answer from Nigel. I have not seen any reply on the phenixbb list so I replied as well. OK, it sounds like the problem is solved!
All the best! Pavel
On 4/18/24 18:00, Jorge Iulek wrote:
Dear Pavel,
Thank you; Nigel has also written me, I have tested according to your directions and it works. One has to setup up cld=False as you point (but this is not needed for angles, dihedrals). Sincerely,
Jorge
On 4/18/24 21:35, Pavel Afonine wrote:
Hi Jorge,
to answer your question and for the record, the following exercise:
phenix.fetch_pdb 1yjp --mtz phenix.refine 1yjp.{pdb,mtz} output.prefix=1 params.eff write_final_geo_file=true > & 1.zlog & phenix.refine 1yjp.{pdb,mtz} output.prefix=2 params.eff write_final_geo_file=true cdl=false > & 2.zlog &
confirms that you can override standard bond lengths and sigmas.
In the first case I see (both geo files):
User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 1.456 1.459 -0.003 1.21e-02 6.83e+03 4.30e-02
and
User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 1.458 1.458 -0.000 1.19e-02 7.06e+03 2.44e-04
And in the second case I see
User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 2.000 1.459 0.541 1.00e-02 1.00e+04 2.93e+03
and
User supplied restraints: 1 Sorted by residual: bond pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 2.000 1.987 0.013 1.00e-02 1.00e+04 1.79e+00
NOTE the nuance: you need to disable CDL for this to work as you want.
Pavel
On 4/16/24 11:23, Jorge Iulek wrote:
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
phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
participants (3)
-
Jorge Iulek -
Nigel Moriarty -
Pavel Afonine