7. Re: density level (Nathaniel Echols)
   9. Re: density level (Pavel Afonine)



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Message: 7
Date: Sun, 13 Jan 2013 12:21:00 -0800
From: Nathaniel Echols <nechols@lbl.gov>
To: PHENIX user mailing list <phenixbb@phenix-online.org>
Subject: Re: [phenixbb] density level
Message-ID:
        <CALeAa1Mty9=U-CFcmhJ1ZRWAiuXMeOS0RHVT4YtXpOVBO0EDyQ@mail.gmail.com>
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On Sun, Jan 13, 2013 at 11:38 AM, CPMAS Chen <cpmasmit@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




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Message: 9
Date: Sun, 13 Jan 2013 21:19:17 -0800
From: Pavel Afonine <pafonine@lbl.gov>
To: PHENIX user mailing list <phenixbb@phenix-online.org>
Subject: Re: [phenixbb] density level
Message-ID: <50F39555.8000000@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@phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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