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Hello, I have a ligand bound to a heme and I have supplied a CIF for phenix in refinement. I did not include all atoms just, those close to the iron. Unfortunately, I am getting very large reported bond deviations for other atoms. For example I get: bond pdb="FE HEM A 410 " pdb=" N3 CPZ A 500 " ideal model delta sigma weight residual 2.100 4.054 -1.954 2.00e-01 2.50e+01 9.54e+01 N3 and FE are not bonded and not expected to be close to one another. it is not supported by the structure. I suspect that this is causing my overall bonds deviations to be ~0.03 even if I greatly reduce the weight of wxc. Is it necessary to enter all of these outliers into the .cif file or is there an easier way? Thank you.
![](https://secure.gravatar.com/avatar/e3bdd26d9a8445dd88f3f601ed20f9d1.jpg?s=120&d=mm&r=g)
Hello again,
have fixed the CIF and I still get a large overall bond deviation > 0.03,
even when using wxc_scale = 0.02. It does not change much even though the
angle sigmas move from 1.4 to about 0.7.
Is there anyway to set a target of say, .0015 and optimize the R/Rfree
around this? My resolution is 2.5 A. Is it possible I am over parametizing
using isotropic B factor refinement and individual coordinate refinement? I
estitmate my parameter/obs ratio to be ~ 1.5. I have an unusuallyl large
solvent content, about 65%.
On Monday, June 23, 2014, Yarrow Madrona
Hello,
I have a ligand bound to a heme and I have supplied a CIF for phenix in refinement. I did not include all atoms just, those close to the iron. Unfortunately, I am getting very large reported bond deviations for other atoms. For example I get:
bond pdb="FE HEM A 410 " pdb=" N3 CPZ A 500 " ideal model delta sigma weight residual 2.100 4.054 -1.954 2.00e-01 2.50e+01 9.54e+01
N3 and FE are not bonded and not expected to be close to one another. it is not supported by the structure. I suspect that this is causing my overall bonds deviations to be ~0.03 even if I greatly reduce the weight of wxc.
Is it necessary to enter all of these outliers into the .cif file or is there an easier way? Thank you.
![](https://secure.gravatar.com/avatar/7984547b53fca6ae837ba286f9c92e29.jpg?s=120&d=mm&r=g)
Hi Yarrow, I can have a look if you send me all inputs: data, model and CIF files, as well as any parameter files (if used). Pavel On 6/23/14, 5:42 PM, Yarrow Madrona wrote:
Hello again,
have fixed the CIF and I still get a large overall bond deviation > 0.03, even when using wxc_scale = 0.02. It does not change much even though the angle sigmas move from 1.4 to about 0.7.
Is there anyway to set a target of say, .0015 and optimize the R/Rfree around this? My resolution is 2.5 A. Is it possible I am over parametizing using isotropic B factor refinement and individual coordinate refinement? I estitmate my parameter/obs ratio to be ~ 1.5. I have an unusuallyl large solvent content, about 65%.
On Monday, June 23, 2014, Yarrow Madrona
mailto:[email protected]> wrote: Hello,
I have a ligand bound to a heme and I have supplied a CIF for phenix in refinement. I did not include all atoms just, those close to the iron. Unfortunately, I am getting very large reported bond deviations for other atoms. For example I get:
bond pdb="FE HEM A 410 " pdb=" N3 CPZ A 500 " ideal model delta sigma weight residual 2.100 4.054 -1.954 2.00e-01 2.50e+01 9.54e+01
N3 and FE are not bonded and not expected to be close to one another. it is not supported by the structure. I suspect that this is causing my overall bonds deviations to be ~0.03 even if I greatly reduce the weight of wxc.
Is it necessary to enter all of these outliers into the .cif file or is there an easier way? Thank you.
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
![](https://secure.gravatar.com/avatar/e3bdd26d9a8445dd88f3f601ed20f9d1.jpg?s=120&d=mm&r=g)
Hi again,
So the problem has been solved by adding a bond line into the CIF that
explicitely tells phenix that the "bond" should be 4 angstroms instead of
2.1. But I don't understand why Phenix would somehow see that these atoms
should be bonded together. This is a phenyl immidazole ligand with two
nitrogens, one of which is about 1.9 angstroms from the iron (a real
coordination). The other is about 4 angstroms. Why does phenix seem to want
to assign a bond between the nitrogen further away?
-Yarrow
On Monday, June 23, 2014, Yarrow Madrona
Hello,
I have a ligand bound to a heme and I have supplied a CIF for phenix in refinement. I did not include all atoms just, those close to the iron. Unfortunately, I am getting very large reported bond deviations for other atoms. For example I get:
bond pdb="FE HEM A 410 " pdb=" N3 CPZ A 500 " ideal model delta sigma weight residual 2.100 4.054 -1.954 2.00e-01 2.50e+01 9.54e+01
N3 and FE are not bonded and not expected to be close to one another. it is not supported by the structure. I suspect that this is causing my overall bonds deviations to be ~0.03 even if I greatly reduce the weight of wxc.
Is it necessary to enter all of these outliers into the .cif file or is there an easier way? Thank you.
![](https://secure.gravatar.com/avatar/e1068d4e9bf58f2b9a630bdc97e3773f.jpg?s=120&d=mm&r=g)
Yarrow
The inputs are likely telling it to form the bond as it's not an automatic
thing. Please send all inputs to Pavel and I, off-line.
Cheers
Nigel
On Mon, Jun 23, 2014 at 6:03 PM, Yarrow Madrona
Hi again,
So the problem has been solved by adding a bond line into the CIF that explicitely tells phenix that the "bond" should be 4 angstroms instead of 2.1. But I don't understand why Phenix would somehow see that these atoms should be bonded together. This is a phenyl immidazole ligand with two nitrogens, one of which is about 1.9 angstroms from the iron (a real coordination). The other is about 4 angstroms. Why does phenix seem to want to assign a bond between the nitrogen further away?
-Yarrow
On Monday, June 23, 2014, Yarrow Madrona
wrote: Hello,
I have a ligand bound to a heme and I have supplied a CIF for phenix in refinement. I did not include all atoms just, those close to the iron. Unfortunately, I am getting very large reported bond deviations for other atoms. For example I get:
bond pdb="FE HEM A 410 " pdb=" N3 CPZ A 500 " ideal model delta sigma weight residual 2.100 4.054 -1.954 2.00e-01 2.50e+01 9.54e+01
N3 and FE are not bonded and not expected to be close to one another. it is not supported by the structure. I suspect that this is causing my overall bonds deviations to be ~0.03 even if I greatly reduce the weight of wxc.
Is it necessary to enter all of these outliers into the .cif file or is there an easier way? Thank you.
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov
participants (3)
-
Nigel Moriarty
-
Pavel Afonine
-
Yarrow Madrona