Hello, I am refining a structure using a.eff file that I generated in Phenix version 1.7 GUI and later ran in the command line. When I try to run the same refinement in Phenix V.1.8 I get the following error: For French and Wilson scaling, sigma_iobs_rejection_criterion must be set between -4.0 and -1.0 I see that it was set to zero previously. My questions are: 1. Is this the same observed criterion that is reported in the RCSB Deposition? 2. To be honest I don't understand what this is. Is it a limit for the error in Iobs, below which the reflection will be discarded? 3. What is a reasonable setting for this input and how does it change the refinement? Thank you (I appreciate your help as I know these may be very basic questions). -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
On Tue, Jul 10, 2012 at 8:58 AM, Yarrow Madrona
1. Is this the same observed criterion that is reported in the RCSB Deposition?
2. To be honest I don't understand what this is. Is it a limit for the error in Iobs, below which the reflection will be discarded?
3. What is a reasonable setting for this input and how does it change the refinement?
To be honest, this was an incompatibility between the current code and older parameter files that we hadn't anticipated. In the context of French & Wilson treatment, I believe the parameter basically filters out excessively negative intensities. I would probably leave this alone - you can get the old parameter file to work again by resetting it to None, which is the new default value. The current nightly build has been fixed to prevent it from stopping if it sees a value of 0 instead. -Nat
Thaank you Nat, This solves my problem.
On Tue, Jul 10, 2012 at 8:58 AM, Yarrow Madrona
wrote: 1. Is this the same observed criterion that is reported in the RCSB Deposition?
2. To be honest I don't understand what this is. Is it a limit for the error in Iobs, below which the reflection will be discarded?
3. What is a reasonable setting for this input and how does it change the refinement?
To be honest, this was an incompatibility between the current code and older parameter files that we hadn't anticipated. In the context of French & Wilson treatment, I believe the parameter basically filters out excessively negative intensities. I would probably leave this alone - you can get the old parameter file to work again by resetting it to None, which is the new default value. The current nightly build has been fixed to prevent it from stopping if it sees a value of 0 instead.
-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
Hi, Do you know where I could find the default values for criteria for error in Iobs and Fobs? I am having trouble finding it in the log file. Thanks. -Yarrow
On Tue, Jul 10, 2012 at 8:58 AM, Yarrow Madrona
wrote: 1. Is this the same observed criterion that is reported in the RCSB Deposition?
2. To be honest I don't understand what this is. Is it a limit for the error in Iobs, below which the reflection will be discarded?
3. What is a reasonable setting for this input and how does it change the refinement?
To be honest, this was an incompatibility between the current code and older parameter files that we hadn't anticipated. In the context of French & Wilson treatment, I believe the parameter basically filters out excessively negative intensities. I would probably leave this alone - you can get the old parameter file to work again by resetting it to None, which is the new default value. The current nightly build has been fixed to prevent it from stopping if it sees a value of 0 instead.
-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
Hi Yarrow, if you run refinement with F, then only F>=0 are used. If you run refinement with I, then the French&Wilson procedure of converting I to F is used: French, G.S., Wilson, K.S. (1978) On the treatment of negative intensity observations. Acta Cryst A34, 517–525. Pavel On 7/10/12 2:38 PM, Yarrow Madrona wrote:
Hi,
Do you know where I could find the default values for criteria for error in Iobs and Fobs? I am having trouble finding it in the log file. Thanks.
-Yarrow
1. Is this the same observed criterion that is reported in the RCSB Deposition?
2. To be honest I don't understand what this is. Is it a limit for the error in Iobs, below which the reflection will be discarded?
3. What is a reasonable setting for this input and how does it change the refinement? To be honest, this was an incompatibility between the current code and
On Tue, Jul 10, 2012 at 8:58 AM, Yarrow Madrona
wrote: older parameter files that we hadn't anticipated. In the context of French & Wilson treatment, I believe the parameter basically filters out excessively negative intensities. I would probably leave this alone - you can get the old parameter file to work again by resetting it to None, which is the new default value. The current nightly build has been fixed to prevent it from stopping if it sees a value of 0 instead. -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
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Nathaniel Echols
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Pavel Afonine
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Yarrow Madrona