[phenixbb] Electron Density

[CPMAS Chen]

Thanks, Nat,

If the density level(map or coefficient) of phenix is not an absolute
level, then I really do not need to worry what shows up by coot.

I used the Fourier map generated by phenix, .mtz file.

Thanks!

   6. density level (CPMAS Chen)

>    7. Re: density level (Nathaniel Echols)
>    9. Re: density level (Pavel Afonine)
>
>
>
> ------------------------------
>
>
> Message: 7
> Date: Sun, 13 Jan 2013 12:21:00 -0800
> From: Nathaniel Echols <nechols at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] density level
> Message-ID:
>         <CALeAa1Mty9=
> U-CFcmhJ1ZRWAiuXMeOS0RHVT4YtXpOVBO0EDyQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Sun, Jan 13, 2013 at 11:38 AM, CPMAS Chen <cpmasmit at gmail.com> wrote:
> > I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To my
> > surprise, the absolute electron density on the 2Fo-Fc map is quite
> > different.
>
> The electron density maps (or coefficients) generated by Phenix are
> not on an absolute scale, and the values displayed by Coot are more or
> less irrelevant.  The scaling method changed significantly between
> 1.6.4 and 1.8, so I'm not surprised that the map levels did too.
>
> > By the way, is there a simple way to keep only F and SIGF column of the
> > autoxds generated truncate.mtz via phenix? the GUI does not allow to
> reduce
> > columns. I normally use IMEAN and SIGIMEAN to do refinement, but this may
> > not be necessary as it is pointed in the maillist, since the intensity is
> > already transformed to amplitude after truncation in autoxds.
> >
> > I can specify labels by xray_data.labels = "F, SIGF", but apparently
> phenix
> > treats it as containing anomalous data. the following is extracted from
> the
> > refine pdb file
> >
> > MIN(FOBS/SIGMA_FOBS)              : 1.16
> > REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.11
> > REMARK   3   NUMBER OF REFLECTIONS             : 143207
> > REMARK   3   NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247
> >
> > Also, in the auto generated def file,
> > xray_data.labels = "F, SIGF, DANO, SIGDANO"
>
> This is intentional - why would you want to throw out information?
> However, you can always use either the reflection file editor (in the
> latest builds) or the French & Wilson GUI to convert IMEAN to F.
>
>




> -Nat
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Sun, 13 Jan 2013 21:19:17 -0800
> From: Pavel Afonine <pafonine at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] density level
> Message-ID: <50F39555.8000000 at lbl.gov>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi,
>
> what kind of file you use to see the map in Coot: Fourier map
> coefficients (MTZ file) or actual map (CCP4 binary formatted file with
> the map)? I need to know this before offering a first guess on what may
> be the reason for this.
>
> Pavel
>
> On 1/13/13 11:38 AM, CPMAS Chen wrote:
> > Dear PhenixBBer,
> >
> > I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To
> > my surprise, the absolute electron density on the 2Fo-Fc map is quite
> > different.
> >
> > https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png
> >
> > At the same sigma level(1.5), the absolute density of the violet map
> > is 0.32e/A^3 (phenix-dev-1266), while that of the blue map is
> > 0.01e/A^3(phenix-1.6.4-486). Besides the different phenix used, there
> > is no other difference on the data and model used.
> >
> > Sam encountered a similar problem on the density.
> >
> > http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html
> >
> > By the way, is there a simple way to keep only F and SIGF column of
> > the autoxds generated truncate.mtz via phenix? the GUI does not allow
> > to reduce columns. I normally use IMEAN and SIGIMEAN to do refinement,
> > but this may not be necessary as it is pointed in the maillist, since
> > the intensity is already transformed to amplitude after truncation in
> > autoxds.
> >
> > I can specify labels by xray_data.labels = "F, SIGF", but apparently
> > phenix treats it as containing anomalous data. the following is
> > extracted from the refine pdb file
> >
> > MIN(FOBS/SIGMA_FOBS)              : 1.16
> > REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.11
> > REMARK   3   NUMBER OF REFLECTIONS             : 143207
> > REMARK   3   NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247
> >
> > Also, in the auto generated def file,
> > xray_data.labels = "F, SIGF, DANO, SIGDANO"
> >
> > Or there is a work round for this issue?
> >
> > Thanks!
> >
> > --
> >
> > ***************************************************
> >
> > Charles Chen
> >
> > Research Associate
> >
> > University of Pittsburgh School of Medicine
> >
> > Department of Anesthesiology
> >
> > ******************************************************
> >
> >
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
>
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> ------------------------------
>
> ***************************************************

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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