Does phenix have a reflection file utility for correctly inverting a set of phase angles? Blaine Mooers Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: [email protected]mailto:[email protected] webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/g...
Hi Blaine, I don't think we have any tool that will do this in a general way, no. I can think of several possibilities of what you might want to do: (1) Change phases corresponding to swapping all anomalous differences. I think that this is not possible without having access to the original data and sites because the phases come partly from anomalous differences and partly from the heavy-atom substructure. (2) Change phases corresponding to inverting heavy-atom substructure. This is done automatically in Phaser when you run SAD phasing (it can output both sets of phases). (3) Change phases corresponding to inverting the structure. This one is easy but doesn't seem likely to be interesting or useful. Would you be wanting one of these or something else? All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Mooers, Blaine H.M. (HSC) [[email protected]] Sent: Thursday, April 19, 2012 10:53 AM To: [email protected] Subject: [phenixbb] inverting a set of phase angles Does phenix have a reflection file utility for correctly inverting a set of phase angles? Blaine Mooers Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: [email protected]mailto:[email protected] webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/g...
Hi Tom, (3) is what I am after. I want to calculate the mean phase error between the phases for the correct hand and a reference set of phases so the phases are of interest here. I thought I only had to shift the phases by 180 degrees to invert the hand. The resulting map looks much poorer. The space group is R32 (the H setting). My fortran jiffy is listed below. Best regards, Blaine real fobs,fom integer h,k,l, phs, nnphs, dphs C open(unit=5,FILE='711pat.phs') open(unit=6,FILE='711_inverted.phs') 3 FORMAT(3i4,F8.2,F8.4,I5) 4 FORMAT(3i4,F8.2,F8.4,I5) 5 FORMAT(3i4,F8.2,F8.4,F8.1) 11 read(5,3,end=9999) h,k,l,fobs,fom,dphs if ((dphs.eq.0).OR.(dphs.eq.360)) then nnphs=180 elseif (dphs.eq.180) then nnphs=0 elseif ((dphs.gt.0).AND.(dphs.lt.180)) then nnphs = dphs + 180 elseif ((dphs.gt.180).AND.(dphs.lt.360))then nnphs = dphs - 180 endif write(6,4) h,k,l,fobs,fom,nnphs goto 11 9999 continue end On Apr 19, 2012, at 12:42 PM, Terwilliger, Thomas C wrote: Hi Blaine, I don't think we have any tool that will do this in a general way, no. I can think of several possibilities of what you might want to do: (1) Change phases corresponding to swapping all anomalous differences. I think that this is not possible without having access to the original data and sites because the phases come partly from anomalous differences and partly from the heavy-atom substructure. (2) Change phases corresponding to inverting heavy-atom substructure. This is done automatically in Phaser when you run SAD phasing (it can output both sets of phases). (3) Change phases corresponding to inverting the structure. This one is easy but doesn't seem likely to be interesting or useful. Would you be wanting one of these or something else? All the best, Tom T ________________________________ From: [email protected]mailto:[email protected] [[email protected]] on behalf of Mooers, Blaine H.M. (HSC) [[email protected]] Sent: Thursday, April 19, 2012 10:53 AM To: [email protected]mailto:[email protected] Subject: [phenixbb] inverting a set of phase angles Does phenix have a reflection file utility for correctly inverting a set of phase angles? Blaine Mooers Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: [email protected]mailto:[email protected] webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/g... _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Blaine, Instead of adding 180 degrees, try multiplying the phase by -1. That should do it. All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Mooers, Blaine H.M. (HSC) [[email protected]] Sent: Thursday, April 19, 2012 12:58 PM To: PHENIX user mailing list Subject: Re: [phenixbb] inverting a set of phase angles Hi Tom, (3) is what I am after. I want to calculate the mean phase error between the phases for the correct hand and a reference set of phases so the phases are of interest here. I thought I only had to shift the phases by 180 degrees to invert the hand. The resulting map looks much poorer. The space group is R32 (the H setting). My fortran jiffy is listed below. Best regards, Blaine real fobs,fom integer h,k,l, phs, nnphs, dphs C open(unit=5,FILE='711pat.phs') open(unit=6,FILE='711_inverted.phs') 3 FORMAT(3i4,F8.2,F8.4,I5) 4 FORMAT(3i4,F8.2,F8.4,I5) 5 FORMAT(3i4,F8.2,F8.4,F8.1) 11 read(5,3,end=9999) h,k,l,fobs,fom,dphs if ((dphs.eq.0).OR.(dphs.eq.360)) then nnphs=180 elseif (dphs.eq.180) then nnphs=0 elseif ((dphs.gt.0).AND.(dphs.lt.180)) then nnphs = dphs + 180 elseif ((dphs.gt.180).AND.(dphs.lt.360))then nnphs = dphs - 180 endif write(6,4) h,k,l,fobs,fom,nnphs goto 11 9999 continue end On Apr 19, 2012, at 12:42 PM, Terwilliger, Thomas C wrote: Hi Blaine, I don't think we have any tool that will do this in a general way, no. I can think of several possibilities of what you might want to do: (1) Change phases corresponding to swapping all anomalous differences. I think that this is not possible without having access to the original data and sites because the phases come partly from anomalous differences and partly from the heavy-atom substructure. (2) Change phases corresponding to inverting heavy-atom substructure. This is done automatically in Phaser when you run SAD phasing (it can output both sets of phases). (3) Change phases corresponding to inverting the structure. This one is easy but doesn't seem likely to be interesting or useful. Would you be wanting one of these or something else? All the best, Tom T ________________________________ From: [email protected]mailto:[email protected] [[email protected]] on behalf of Mooers, Blaine H.M. (HSC) [[email protected]] Sent: Thursday, April 19, 2012 10:53 AM To: [email protected]mailto:[email protected] Subject: [phenixbb] inverting a set of phase angles Does phenix have a reflection file utility for correctly inverting a set of phase angles? Blaine Mooers Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: [email protected]mailto:[email protected] webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/g... _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Tom, That solved my problem. I am obviously getting rusty on the basics. Best regards, Blaine On Apr 19, 2012, at 2:09 PM, Terwilliger, Thomas C wrote: Hi Blaine, Instead of adding 180 degrees, try multiplying the phase by -1. That should do it. All the best, Tom T ________________________________ From: [email protected]mailto:[email protected] [[email protected]] on behalf of Mooers, Blaine H.M. (HSC) [[email protected]] Sent: Thursday, April 19, 2012 12:58 PM To: PHENIX user mailing list Subject: Re: [phenixbb] inverting a set of phase angles Hi Tom, (3) is what I am after. I want to calculate the mean phase error between the phases for the correct hand and a reference set of phases so the phases are of interest here. I thought I only had to shift the phases by 180 degrees to invert the hand. The resulting map looks much poorer. The space group is R32 (the H setting). My fortran jiffy is listed below. Best regards, Blaine real fobs,fom integer h,k,l, phs, nnphs, dphs C open(unit=5,FILE='711pat.phs') open(unit=6,FILE='711_inverted.phs') 3 FORMAT(3i4,F8.2,F8.4,I5) 4 FORMAT(3i4,F8.2,F8.4,I5) 5 FORMAT(3i4,F8.2,F8.4,F8.1) 11 read(5,3,end=9999) h,k,l,fobs,fom,dphs if ((dphs.eq.0).OR.(dphs.eq.360)) then nnphs=180 elseif (dphs.eq.180) then nnphs=0 elseif ((dphs.gt.0).AND.(dphs.lt.180)) then nnphs = dphs + 180 elseif ((dphs.gt.180).AND.(dphs.lt.360))then nnphs = dphs - 180 endif write(6,4) h,k,l,fobs,fom,nnphs goto 11 9999 continue end On Apr 19, 2012, at 12:42 PM, Terwilliger, Thomas C wrote: Hi Blaine, I don't think we have any tool that will do this in a general way, no. I can think of several possibilities of what you might want to do: (1) Change phases corresponding to swapping all anomalous differences. I think that this is not possible without having access to the original data and sites because the phases come partly from anomalous differences and partly from the heavy-atom substructure. (2) Change phases corresponding to inverting heavy-atom substructure. This is done automatically in Phaser when you run SAD phasing (it can output both sets of phases). (3) Change phases corresponding to inverting the structure. This one is easy but doesn't seem likely to be interesting or useful. Would you be wanting one of these or something else? All the best, Tom T ________________________________ From: [email protected]mailto:[email protected] [[email protected]] on behalf of Mooers, Blaine H.M. (HSC) [[email protected]] Sent: Thursday, April 19, 2012 10:53 AM To: [email protected]mailto:[email protected] Subject: [phenixbb] inverting a set of phase angles Does phenix have a reflection file utility for correctly inverting a set of phase angles? Blaine Mooers Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: [email protected]mailto:[email protected] webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/g... _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (2)
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Mooers, Blaine H.M. (HSC) -
Terwilliger, Thomas C