[phenixbb] inverting a set of phase angles

[Mooers, Blaine H.M. (HSC)]

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: phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> [phenixbb-bounces at phenix-online.org] on behalf of Mooers, Blaine H.M. (HSC) [Blaine-Mooers at ouhsc.edu]
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: phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> [phenixbb-bounces at phenix-online.org] on behalf of Mooers, Blaine H.M. (HSC) [Blaine-Mooers at ouhsc.edu]
Sent: Thursday, April 19, 2012 10:53 AM
To: phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
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:  blaine-mooers at ouhsc.edu<mailto:blaine-mooers at ouhsc.edu>
webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/general-program-info/faculty/blaine-mooers-ph-d-





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