[ccp4bb] Coot on Macosx Catalina

[Jan van Agthoven]

Hi everyone,
I'm running into issues installing coot on Macosx Catalina. When install the 
system using BINARY.setup the following message shows up:


Does anyone else faced this problem? Is there a way to work around it?
Thanks,
J.


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Re: [ccp4bb] Issues in new Mac version 10.15

[Peter Moody]

Xquartz reinstall works for me, but the CCP4 updater is broken.
At the "Applying changes" step it will seem to pause (although using 100%
of a cpu) and will continue to run despite exiting.
Forced quit is needed (but doesn't seem to do any harm).

Peter
( I am very bad at monitoring this account, please use my university email
address if you want to contact me directly)

On Thu, 17 Oct 2019 at 09:24, Charles Ballard - UKRI STFC <
charles.ball...@stfc.ac.uk> wrote:

> Dear All
>
> as has been pointed out, and as per usual, OS X updates seem to remove
> some of the setup for XQuartz, which will cause most X11 based apps to stop
> working.  It is best to re-install XQuartz.  This will work for an updated
> system that had CCP4 previously installed on it.  We have had a few reports
> of issues when installing on a fresh  10.15 machine through the CCP4
> downloads manager (tarball route still works).  We are investigating.
>
> All the best
>
> Charles
>
> On 16 Oct 2019, at 17:42, Werther, Rachel A wrote:
>
> Thanks to all who gave advice.  The reinstallation of XQuartz worked for
> me.  I was using the most updated version of XQuartz before I reinstalled
> it, but as Guillaume Gaullier told me:
>
> “…macOS updates typically wipe out most files of your XQuartz installation
> (XQuartz.app will still be where it was originally installed, but unlike
> most Mac applications this one is not self-contained and has important
> files under /opt/X11 that get erased by a system update). And Coot requires
> XQuartz to display its window, so this is the most likely explanation for
> why it would not work after a system update.
>
> Try reinstalling XQuartz from https://www.xquartz.org/<
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.xquartz.org_=DwMFaQ=eRAMFD45gAfqt84VtBcfhQ=DO9lvOAiEYffd0DHXxXRFRhnm_KEyAdWVXbYX9zO5B8=zb3XqXe1iBKaPGEDyfZCe-uLxGJJVI0SzgY3of7iAxk=3FyzcByzIrl83gOdCoaiFSzE7Mbhtist6uxzCuQjIXA=>,
> then log out and log back in (or reboot, that should do it too), and see if
> Coot starts up normally.”
>
> Happy solving,
> Rachel
>
> Rachel Werther / Research Technician III / Stoddard Lab / Basic Sciences /
> Fred Hutchinson Cancer Research Center / rwert...@fredhutch.org rwert...@fredhutch.org> / 206-667-4066
>
> From: CCP4 bulletin board  CCP4BB@JISCMAIL.AC.UK>> on behalf of "Werther, Rachel A" <
> rwert...@fredhutch.org>
> Reply-To: "Werther, Rachel A"  rwert...@fredhutch.org>>
> Date: Tuesday, October 15, 2019 at 5:01 PM
> To: "CCP4BB@JISCMAIL.AC.UK" <
> CCP4BB@JISCMAIL.AC.UK>
> Subject: [ccp4bb] Issues in new Mac version 10.15
>
> Hello All,
>
> I downloaded the latest Mac Update, 10.15 Catalina, and then Coot wouldn’t
> open on my computer.
>
> Phenix opened as usual.  I use the GUI, and the button that says “Open in
> COOT” was not greyed out, but would not launch the window.  When I tried to
> open it directly from Finder, it also failed to open.  The cartoon coot
> appeared on my recently opened section of my bottom-of-screen toolbar, but
> nothing happened.
>
> Next I downloaded the latest CCP4-7.0.077, and followed the instructions
> to remove the extended attributes:
> ATTENTION: If you are planning to install CCP4 from a tarball on Mac OS X
> version 10.13 or later (10.12 was not tested), you will have to remove
> extended attributes from the tar-gz-file before unpacking it, otherwise the
> app icons will not be functional (and you will be able to launch the CCP4
> apps including ccp4i and ccp4i2 from the command line only). The extended
> attributes can be removed from the file _file_ using the command "xattr -c
> _file_". For example: xattr -c ccp4-7.0.065-macosx64.tar.gz
>
> But when I try to open CCP4, I get this message:
> Ccp4 cannot be opened because of a problem.
> Check with the developer to make sure ccp4 works with this version of
> macOS. You may need to reinstall the application. Be sure to install any
> available updates for the application and macOS.
> Click Report to see more detailed information and send a report to Apple.
>
> And when I try to open Coot from the Finder, I again just see the icon in
> my recently opened section of my bottom-of-screen toolbar, but it doesn’t
> open.
>
> Any advice?
>
> Many thanks,
> Rachel
>
> Rachel Werther / Research Technician III / Stoddard Lab / Basic Sciences /
> Fred Hutchinson Cancer Research Center / rwert...@fredhutch.org rwert...@fredhutch.org> / 206-667-4066
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMGaQ=eRAMFD45gAfqt84VtBcfhQ=DO9lvOAiEYffd0DHXxXRFRhnm_KEyAdWVXbYX9zO5B8=DLlHXm0LUKHS_PFqce1iCejwGvyoaCkFpJGwuJyob_Q=HfIn8TsXm95kj-mZzZ_fHbCh2I6Lzu3-v2XlHisInZQ=
> >
>
> 

Re: [ccp4bb] Figure of merit in refinement

[Randy Read]

Dear Eleanor,

Yes, difference maps are weighted by FOM, with the coefficient being m*Fo-D*Fc, 
phased by the model. If Fc is small, then m will be small because, even if Fo 
is large, you have no idea what phase to assign to the difference.  If Fc is 
large because you haven't treated bulk solvent, it turns out that D will 
effectively apply a Babinet scaling because D includes a term with the square 
root of the mean observed intensity divided by the mean calculated intensity.  
If Fc is large even with a bulk solvent correction, then you want a big 
negative term in the difference coefficient so that's fine too!

Best wishes,

Randy

> On 18 Oct 2019, at 07:31, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> This is hunch speak - not proper analysis, but it is possible to get huge 
> Fcalc, and hence large difference map terms,  at low resolution by assuming 
> the solvent volume is a vacuum, not full of partially ordered water 
> molecules. 
> The Babinet scaling can do something to correct this but it is a very blunt 
> tool.  And once a structure is more or less complete the Solvent masked 
> contribution to Fcalc helps, but there is an intermediate stage where 
> spurious differences can distort maps.
> 
> As Randy says - if either Eobs or Ecalc is small the FOM is also small. The 
> worst offenders are when Eobs is large but Ecalc is crazy. 
> I like to look at the plot of  v v resolution,  output by REFMAC 
> along with Rfactor plots. If thee are large discrepancies
> maybe it is time to worry about scaling options..
> 
> Eleanor
> 
> PS - But are difference map terms weighted by FOM? 
> 
> 
> On Thu, 17 Oct 2019 at 08:55, Jan Dohnalek  > wrote:
> Dear all,
> regarding the "remaining strong differences" between measured data and 
> calculated SFs from a a finished (high res structure) I once investigated a 
> bit into this going back to images and looking up some extreme outliers.
> I found the same - those were clear strong diffraction spots, not ice, not 
> small molecule, genuine protein diffraction. So I had no explanation for 
> those. Some were even "forbidden" intensities, because of screw axes which 
> were correct. structure refined perfectly, no problems at all.
> I then found some literature about the possibilities of multiple reflections 
> - I guess this is possible but I wonder if you could get easily say a 25 
> sigma I in this way.
> 
> And as we often end our beer-discussions - may be all protein space groups 
> are actually true P1, just close enough to satisfy the high symmetry rules .. 
> but this is getting a bit philosophical I know ..
> 
> Jan Dohnalek
> 
> 
> 
> 
> On Wed, Oct 16, 2019 at 6:24 PM Randy Read  > wrote:
> James,
> 
> Where we diverge is with your interpretation that big differences lead to 
> small FOMs.  The size of the FOM depends on the product of Fo and Fc, not 
> their difference.  The FOM for a reflection where Fo=1000 and Fc=10 is very 
> different from the FOM for a reflection with Fo=5000 and Fc=4010, even though 
> the difference is the same.
> 
> Expanding on this: 
> 
> 1. The FOM actually depends more on the E values, i.e. reflections smaller 
> than average get lower FOM values than ones bigger than average.  In the 
> resolution bin from 5.12 to 5.64Å of 2vb1, the mean observed intensity is 
> 20687 and the mean calculated intensity is 20022, which means that 
> Eobs=Sqrt(145.83/20687)=0.084 and Ecalc=Sqrt(7264/20022)=0.602.  This 
> reflection gets a low FOM because the product (0.050) is such a small number, 
> not because the difference is big.
> 
> 2. You have to consider the role of the model error in the difference, 
> because for precisely-measured data most of the difference comes from model 
> error.  In this resolution shell, the correlation coefficient between Iobs 
> and Fcalc^2 is about 0.88, which means that sigmaA is about Sqrt(0.88) = 
> 0.94.  The variance of both the real and imaginary components of Ec (as an 
> estimate of the phased true E) will be (1-0.94^2)/2 = 0.058, so the standard 
> deviations of the real and imaginary components of Ec will be about 0.24.  In 
> that context, the difference between Eobs and Ecalc is nothing like a 
> 2000-sigma outlier.
> 
> Looking at this another way, the reason why the FOM is low for this 
> reflection is that the conditional probability distribution of Eo given Ec 
> has significant values on the other side of the origin of the complex plane. 
> That means that the *phase* of the complex Eo is very uncertain.  The figures 
> in this web page 
> (https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html 
> ) 
> should help to explain that idea.
> 
> Best wishes,
> 
> Randy
> 
>> On 16 Oct 2019, at 16:02, James Holton > > wrote:
>> 
>> 
>> All very true Randy,
>> 
>> But nevertheless every hkl 

Re: [ccp4bb] Figure of merit in refinement

[Eleanor Dodson]

This is hunch speak - not proper analysis, but it is possible to get huge
Fcalc, and hence large difference map terms,  at low resolution by assuming
the solvent volume is a vacuum, not full of partially ordered water
molecules.
The Babinet scaling can do something to correct this but it is a very blunt
tool.  And once a structure is more or less complete the Solvent masked
contribution to Fcalc helps, but there is an intermediate stage where
spurious differences can distort maps.

As Randy says - if either Eobs or Ecalc is small the FOM is also small. The
worst offenders are when Eobs is large but Ecalc is crazy.
I like to look at the plot of  v v resolution,  output by
REFMAC along with Rfactor plots. If thee are large discrepancies
maybe it is time to worry about scaling options..

Eleanor

PS - But are difference map terms weighted by FOM?


On Thu, 17 Oct 2019 at 08:55, Jan Dohnalek  wrote:

> Dear all,
> regarding the "remaining strong differences" between measured data and
> calculated SFs from a a finished (high res structure) I once investigated a
> bit into this going back to images and looking up some extreme outliers.
> I found the same - those were clear strong diffraction spots, not ice, not
> small molecule, genuine protein diffraction. So I had no explanation for
> those. Some were even "forbidden" intensities, because of screw axes which
> were correct. structure refined perfectly, no problems at all.
> I then found some literature about the possibilities of multiple
> reflections - I guess this is possible but I wonder if you could get easily
> say a 25 sigma I in this way.
>
> And as we often end our beer-discussions - may be all protein space groups
> are actually true P1, just close enough to satisfy the high symmetry rules
> .. but this is getting a bit philosophical I know ..
>
> Jan Dohnalek
>
>
>
>
> On Wed, Oct 16, 2019 at 6:24 PM Randy Read  wrote:
>
>> James,
>>
>> Where we diverge is with your interpretation that big differences lead to
>> small FOMs.  The size of the FOM depends on the product of Fo and Fc, not
>> their difference.  The FOM for a reflection where Fo=1000 and Fc=10 is very
>> different from the FOM for a reflection with Fo=5000 and Fc=4010, even
>> though the difference is the same.
>>
>> Expanding on this:
>>
>> 1. The FOM actually depends more on the E values, i.e. reflections
>> smaller than average get lower FOM values than ones bigger than average.
>> In the resolution bin from 5.12 to 5.64Å of 2vb1, the mean observed
>> intensity is 20687 and the mean calculated intensity is 20022, which means
>> that Eobs=Sqrt(145.83/20687)=0.084 and Ecalc=Sqrt(7264/20022)=0.602.  This
>> reflection gets a low FOM because the product (0.050) is such a small
>> number, not because the difference is big.
>>
>> 2. You have to consider the role of the model error in the difference,
>> because for precisely-measured data most of the difference comes from model
>> error.  In this resolution shell, the correlation coefficient between Iobs
>> and Fcalc^2 is about 0.88, which means that sigmaA is about Sqrt(0.88) =
>> 0.94.  The variance of both the real and imaginary components of Ec (as an
>> estimate of the phased true E) will be (1-0.94^2)/2 = 0.058, so the
>> standard deviations of the real and imaginary components of Ec will be
>> about 0.24.  In that context, the difference between Eobs and Ecalc is
>> nothing like a 2000-sigma outlier.
>>
>> Looking at this another way, the reason why the FOM is low for this
>> reflection is that the conditional probability distribution of Eo given Ec
>> has significant values on the other side of the origin of the complex
>> plane. That means that the *phase* of the complex Eo is very uncertain.
>> The figures in this web page (
>> https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html)
>> should help to explain that idea.
>>
>> Best wishes,
>>
>> Randy
>>
>> On 16 Oct 2019, at 16:02, James Holton  wrote:
>>
>>
>> All very true Randy,
>>
>> But nevertheless every hkl has an FOM assigned to it, and that is used to
>> calculate the map.  Statistical distribution or not, the trend is that hkls
>> with big amplitude differences get smaller FOMs, so that means large
>> model-to-data discrepancies are down-weighted.  I wonder sometimes at what
>> point this becomes a self-fulfilling prophecy?  If you look in detail and
>> the Fo-Fc differences in pretty much any refined structure in the PDB you
>> will find huge outliers.  Some are hundreds of sigmas, and they can go in
>> either direction.
>>
>> Take for example reflection -5,2,2 in the highest-resolution lysozyme
>> structure in the PDB: 2vb1.  Iobs(-5,2,2) was recorded as 145.83 ± 3.62 (at
>> 5.4 Ang) with Fcalc^2(-5,2,2) = 7264.  A 2000-sigma outlier!  What are the
>> odds?   On the other hand, Iobs(4,-6,2) = 1611.21 ± 30.67 vs
>> Fcalc^2(4,-6,2) = 73, which is in the opposite direction.  One can always
>> suppose "experimental errors", but ZD sent me these images and I