<div>Thanks, Nat,</div><div><br></div><div>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.</div><div><br></div><div>I used the Fourier map generated by phenix, .mtz file.</div>
<div><br></div><div>Thanks!</div><div><br></div> 6. density level (CPMAS Chen)<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
7. Re: density level (Nathaniel Echols)<br> 9. Re: density level (Pavel Afonine)<br><br>
<br><br>
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<br>
Message: 7<br>
Date: Sun, 13 Jan 2013 12:21:00 -0800<br>
From: Nathaniel Echols <<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>><br>
To: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>
Subject: Re: [phenixbb] density level<br>
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<CALeAa1Mty9=<a href="mailto:U-CFcmhJ1ZRWAiuXMeOS0RHVT4YtXpOVBO0EDyQ@mail.gmail.com">U-CFcmhJ1ZRWAiuXMeOS0RHVT4YtXpOVBO0EDyQ@mail.gmail.com</a>><br>
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<br>
On Sun, Jan 13, 2013 at 11:38 AM, CPMAS Chen <<a href="mailto:cpmasmit@gmail.com">cpmasmit@gmail.com</a>> wrote:<br>
> I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To my<br>
> surprise, the absolute electron density on the 2Fo-Fc map is quite<br>
> different.<br>
<br>
The electron density maps (or coefficients) generated by Phenix are<br>
not on an absolute scale, and the values displayed by Coot are more or<br>
less irrelevant. The scaling method changed significantly between<br>
1.6.4 and 1.8, so I'm not surprised that the map levels did too.<br>
<br>
> By the way, is there a simple way to keep only F and SIGF column of the<br>
> autoxds generated truncate.mtz via phenix? the GUI does not allow to reduce<br>
> columns. I normally use IMEAN and SIGIMEAN to do refinement, but this may<br>
> not be necessary as it is pointed in the maillist, since the intensity is<br>
> already transformed to amplitude after truncation in autoxds.<br>
><br>
> I can specify labels by xray_data.labels = "F, SIGF", but apparently phenix<br>
> treats it as containing anomalous data. the following is extracted from the<br>
> refine pdb file<br>
><br>
> MIN(FOBS/SIGMA_FOBS) : 1.16<br>
> REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11<br>
> REMARK 3 NUMBER OF REFLECTIONS : 143207<br>
> REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247<br>
><br>
> Also, in the auto generated def file,<br>
> xray_data.labels = "F, SIGF, DANO, SIGDANO"<br>
<br>
This is intentional - why would you want to throw out information?<br>
However, you can always use either the reflection file editor (in the<br>
latest builds) or the French & Wilson GUI to convert IMEAN to F.<br>
<br></blockquote><div><br></div><div><br></div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
-Nat<br>
<br>
<br><br>
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<br>
Message: 9<br>
Date: Sun, 13 Jan 2013 21:19:17 -0800<br>
From: Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>><br>
To: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>
Subject: Re: [phenixbb] density level<br>
Message-ID: <<a href="mailto:50F39555.8000000@lbl.gov">50F39555.8000000@lbl.gov</a>><br>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"<br>
<br>
Hi,<br>
<br>
what kind of file you use to see the map in Coot: Fourier map<br>
coefficients (MTZ file) or actual map (CCP4 binary formatted file with<br>
the map)? I need to know this before offering a first guess on what may<br>
be the reason for this.<br>
<br>
Pavel<br>
<br>
On 1/13/13 11:38 AM, CPMAS Chen wrote:<br>
> Dear PhenixBBer,<br>
><br>
> I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To<br>
> my surprise, the absolute electron density on the 2Fo-Fc map is quite<br>
> different.<br>
><br>
> <a href="https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png" target="_blank">https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png</a><br>
><br>
> At the same sigma level(1.5), the absolute density of the violet map<br>
> is 0.32e/A^3 (phenix-dev-1266), while that of the blue map is<br>
> 0.01e/A^3(phenix-1.6.4-486). Besides the different phenix used, there<br>
> is no other difference on the data and model used.<br>
><br>
> Sam encountered a similar problem on the density.<br>
><br>
> <a href="http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html" target="_blank">http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html</a><br>
><br>
> By the way, is there a simple way to keep only F and SIGF column of<br>
> the autoxds generated truncate.mtz via phenix? the GUI does not allow<br>
> to reduce columns. I normally use IMEAN and SIGIMEAN to do refinement,<br>
> but this may not be necessary as it is pointed in the maillist, since<br>
> the intensity is already transformed to amplitude after truncation in<br>
> autoxds.<br>
><br>
> I can specify labels by xray_data.labels = "F, SIGF", but apparently<br>
> phenix treats it as containing anomalous data. the following is<br>
> extracted from the refine pdb file<br>
><br>
> MIN(FOBS/SIGMA_FOBS) : 1.16<br>
> REMARK 3 COMPLETENESS FOR RANGE (%) : 97.11<br>
> REMARK 3 NUMBER OF REFLECTIONS : 143207<br>
> REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247<br>
><br>
> Also, in the auto generated def file,<br>
> xray_data.labels = "F, SIGF, DANO, SIGDANO"<br>
><br>
> Or there is a work round for this issue?<br>
><br>
> Thanks!<br>
><br>
> --<br>
><br>
> ***************************************************<br>
><br>
> Charles Chen<br>
><br>
> Research Associate<br>
><br>
> University of Pittsburgh School of Medicine<br>
><br>
> Department of Anesthesiology<br>
><br>
> ******************************************************<br>
><br>
><br>
><br>
> _______________________________________________<br>
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> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
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<p></p><p>***************************************************</p><p>Charles Chen</p><p>Research Associate</p><p>University of Pittsburgh School of Medicine</p><p>Department of Anesthesiology</p><p>******************************************************</p>
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