[ccp4bb] SAXS Workshop at BioCAT at teh Advanced Photon Source - Second Notice.

[Thomas Irving]

BioCAT is offering its fifth intensive HOW-TO course in BioSAXS. Students
will have two days of lectures and hands-on software tutorials on the
basics of BioSAXS data collection and processing from expert practitioners
in the field. This will be followed by data collection on the BioCAT
beamline (Sector 18 at the APS) and data analysis help. Students are
encouraged to bring 1-2 research samples for the data collection.

Also, for the first time ever, BioCAT is offering this course for remote
participants. Remote participants will get a live-stream of the lectures,
and all of the tutorial materials. They will not be able to collect data.

The course will take place from 11/5/19-11/7/19 at the APS. Registration
for on-site participants is first come, first served, and limited to the
first 15 registrants due to time constraints on how many users can collect
data during the course. Spaces are still available.

Full information, a link for registration, and the tentative schedule can
be found on our website:
https://www.bio.aps.anl.gov/news/everything-biosaxs-5.html

Thanks,
Tom Irving
Director, BioCAT



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Tenure Track Faculty Position in Cell Biology at Florida State University

[Beth Stroupe]

Dear CCP4 community,

I am pleased to announce the opening of a tenure-track Assistant Professor 
position in Biological Science at Florida State University, specializing 
broadly in Cell Biology. 

Job ID 46496 
(https://jobs.omni.fsu.edu/psc/sprdhr_er/EMPLOYEE/HRMS/c/HRS_HRAM_FL.HRS_CG_SEARCH_FL.GBL?Page=HRS_APP_SCHJOB_FL=U).
 

FSU is ranked 18th amongst public universities by US News & World reports. The 
Department of Biological Science has a long history of expertise in structural 
biology, in particular in the field of cryo-EM, being one of the first 
institutions in the US to acquire a Titan Krios TEM. Tallahassee, the capital 
city of Florida, is located in the beautiful Big Bend region of Florida and 
offers diverse cultural and outdoor recreational activities.

best,
Beth

The Job Posting is as follows:

JOB ID 46496
Department:
Biological Science

Equal Employment Opportunity:
An Equal Opportunity/Access/Affirmative Action/Pro Disabled & Veteran Employer.

FSU's Equal Opportunity Statement can be viewed at:
http://www.hr.fsu.edu/PDF/Publications/diversity/EEO_Statement.pdf

Responsibilities:
The Department of Biological Science at Florida State University invites 
outstanding applications for a tenure-track Assistant Professor in the 
broadly-defined area of Cell Biology. The Department is interested in 
individuals using any experimental system, from cultured cells to organismal, 
to understand fundamental cellular processes using approaches including but not 
limited to correlative light and electron microscopy, high-resolution light 
microscopy, live cell imaging, or genomics. Successful candidates are expected 
to establish an innovative, extramurally-funded research program and contribute 
to undergraduate and graduate education.

Qualifications:
Successful candidates for an Assistant Professor rank will possess at a minimum 
a doctoral degree from an accredited institution or the highest degree 
appropriate in the field of specialization with a demonstrated record of 
achievement in teaching, academic research, and service. Postdoctoral training 
in the field of specialization is preferred.

Other Information:
The Department of Biological Science is a diverse and interactive group with 46 
tenure-track faculty members in Cell and Molecular Biology, Neuroscience, and 
Ecology and Evolution graduate programs. These include scientific leaders in 
cytoskeletal motility, structural biology, epigenetics, chromosome biology, 
plant biology, virology, and chemical senses. Researchers have access to 
excellent core resources, including a state-of-the-art imaging facility 
equipped with a Titan Krios electron microscope, confocals for fixed or live 
cell imaging, and super-resolution 3D-SIM; flow cytometry and mass spectrometry 
facilities; a modern BSL3 facility; and the National High Magnetic Field 
Laboratory.  For information about Florida State University’s Department of 
Biological Science, visit our website at http://www.bio.fsu.edu.

Florida State University is ranked 18th among public universities by US News & 
World Reports. The university is located in Tallahassee, the capital city of 
Florida, which is situated in the Big Bend region of the state, an area with 
diverse and relatively undeveloped habitats. Tallahassee hosts a rich program 
in the performing arts and athletic events and is close to several state parks, 
rivers, a National Wildlife Refuge, the largest national forest in Florida, and 
the pristine beaches of the Gulf of Mexico.

Contact Info:
Questions about the position should be directed to Prof. Hank W. Bass at 
cell.sea...@bio.fsu.edu.

Pay Plan:
This is a Faculty position.

Criminal Background Check:
This position requires successful completion of a criminal history background 
check, to include fingerprinting. The background check will be conducted as 
authorized and in accordance with University Policy 4-OP-C-7-B11.

How To Apply:
If qualified and interested in a specific Faculty job opening as advertised, 
apply to Florida State University at https://jobs.fsu.edu. If you are a current 
FSU employee, apply via myFSU > Self Service. Applicants are required to 
complete the online application with all applicable information. Applications 
must include education details even if attaching a Vita.

Submit with the application a single PDF file with a cover letter, curriculum 
vitae, and statements on research, teaching, and diversity.

This posting will close on December 2, 2019.

Request Letters of Reference:
This position requires that you have three confidential professional letters of 
recommendation submitted on your behalf. Follow the steps below to request 
these letters through our system:

1) After submitting your application, click the Return to Job Search link;
2) Click the My References link; 
3) Click the Send/View Reference Request button next to the appropriate 
position; and 
4) Follow the steps on that page to send your references a system generated 

Re: [ccp4bb] Issues in new Mac version 10.15

[Werther, Rachel A]

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/,
 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 / 206-667-4066

From: CCP4 bulletin board  on behalf of "Werther, Rachel 
A" 
Reply-To: "Werther, Rachel A" 
Date: Tuesday, October 15, 2019 at 5:01 PM
To: "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 / 206-667-4066



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Figure of merit in refinement

[Randy Read]

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 have looked at all 
> the spots involved in these hkls.  I don't see anything wrong with any of 
> them.  The average multiplicity of this data set was 7.1 and involved 3 
> different kappa angles, so I don't think these are "zingers" or other weird 
> measurement problems.
> 
> I'm not just picking on 2vb1 here.  EVERY PDB entry has this problem.  Not 
> sure where it comes from, but the FOM assigned to these huge differences is 
> always small, so whatever is causing them won't show up in an FOM-weighted 
> map.
> 
> Is there a way to "change up" the statistical distribution that assigns FOMs 
> to hkls?  Or are we stuck with this systematic error?
> 
> -James Holton
> MAD Scientist
> 
> On 10/4/2019 9:31 AM, Randy Read wrote:
>> Hi James,
>> 
>> I'm sure you realise this, but it's important for other readers to remember 
>> that the FOM is a statistical quantity: we have a probability distribution 
>> for the true phase, we pick one phase (the "centroid" phase that should 
>> minimise the RMS error in the density map), and then the FOM is the expected 
>> value of the phase error, obtained by taking the cosines of all possible 
>> phase differences and weighting by the probability of that phase difference. 
>>  Because it's a statistical quantity from a random distribution, you really 
>> can't expect this to agree reflection by reflection!  It's a good start to 
>> see that the overall values are good, but if you want to look more closely 
>> you have to look a groups of reflections, e.g. bins of resolution, bins of 
>> observed amplitude, bins of calculated amplitude.  However, each bin has to 
>> have enough members that the average will generally be close to the expected 
>> value.
>> 
>> Best wishes,
>> 
>> Randy Read
>> 
>>> On 4 Oct 2019, at 16:38, James Holton >> > wrote:
>>> 
>>> I've done a few little experiments over the years using simulated data 
>>> where I know the "correct" phase, trying to see just how accurate FOMs are. 
>>> 

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Figure of merit in refinement

[Herman . Schreuder]

Hi James,

Did you ever try what happens if you set all the FOMs of e.g. 2vb1 to 1.0 and 
calculate a map? If you are sure they are not measurement errors they should be 
included in the map. I would expect some huge ripples, but maybe the "outliers" 
compensate and you get a truly interesting map.

Best,
Herman

Von: CCP4 bulletin board  Im Auftrag von James Holton
Gesendet: Mittwoch, 16. Oktober 2019 17:02
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Figure of merit in refinement


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk


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 have looked at all the spots involved in these hkls. 
 I don't see anything wrong with any of them.  The average multiplicity of this 
data set was 7.1 and involved 3 different kappa angles, so I don't think these 
are "zingers" or other weird measurement problems.

I'm not just picking on 2vb1 here.  EVERY PDB entry has this problem.  Not sure 
where it comes from, but the FOM assigned to these huge differences is always 
small, so whatever is causing them won't show up in an FOM-weighted map.

Is there a way to "change up" the statistical distribution that assigns FOMs to 
hkls?  Or are we stuck with this systematic error?

-James Holton
MAD Scientist
On 10/4/2019 9:31 AM, Randy Read wrote:
Hi James,

I'm sure you realise this, but it's important for other readers to remember 
that the FOM is a statistical quantity: we have a probability distribution for 
the true phase, we pick one phase (the "centroid" phase that should minimise 
the RMS error in the density map), and then the FOM is the expected value of 
the phase error, obtained by taking the cosines of all possible phase 
differences and weighting by the probability of that phase difference.  Because 
it's a statistical quantity from a random distribution, you really can't expect 
this to agree reflection by reflection!  It's a good start to see that the 
overall values are good, but if you want to look more closely you have to look 
a groups of reflections, e.g. bins of resolution, bins of observed amplitude, 
bins of calculated amplitude.  However, each bin has to have enough members 
that the average will generally be close to the expected value.

Best wishes,

Randy Read


On 4 Oct 2019, at 16:38, James Holton 
mailto:jmhol...@lbl.gov>> wrote:

I've done a few little experiments over the years using simulated data where I 
know the "correct" phase, trying to see just how accurate FOMs are.  What I 
have found in general is that overall FOM values are fairly well correlated to 
overall phase error, but if you go reflection-by-reflection they are terrible.  
I suppose this is because FOM estimates are rooted in amplitudes.  Good 
agreement in amplitude gives you more confidence in the model (and therefore 
the phases), but if your R factor is 55% then your phases probably aren't very 
good either.  However, if you look at any given h,k,l those assumptions become 
less and less applicable.  Still, it's the only thing we've got.

2qwAt the end of the day, the phase you get out of a refinement program is the 
phase of the model.  All those fancy "FWT" coefficients with "m" and "D" or 
"FOM" weights are modifications to the amplitudes, not the phases.  The phases 
in your 2mFo-DFc map are identical to those of just an Fc map.  Seriously, have 
a look!  Sometimes you will get a 180 flip to keep the sign of the amplitude 
positive, but that's it.  Nevertheless, the electron density of a 2mFo-DFc map 
is closer to the "correct" electron density than any other map.  This is quite 
remarkable considering that the "phase error" is the same.

This realization is what led my colleagues and I to forget about "phase error" 
and start looking at the error in the electron density itself 
(10.1073/pnas.1302823110).  We did this rather pedagogically.  Basically, 
pretend you did the whole experiment again, but "change up" the source of error 
of interest.  For example if you want to see the effect of 

Re: [ccp4bb] Figure of merit in refinement

[James Holton]

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 
have looked at all the spots involved in these hkls.  I don't see 
anything wrong with any of them.  The average multiplicity of this data 
set was 7.1 and involved 3 different kappa angles, so I don't think 
these are "zingers" or other weird measurement problems.


I'm not just picking on 2vb1 here.  EVERY PDB entry has this problem.  
Not sure where it comes from, but the FOM assigned to these huge 
differences is always small, so whatever is causing them won't show up 
in an FOM-weighted map.


Is there a way to "change up" the statistical distribution that assigns 
FOMs to hkls?  Or are we stuck with this systematic error?


-James Holton
MAD Scientist

On 10/4/2019 9:31 AM, Randy Read wrote:

Hi James,

I'm sure you realise this, but it's important for other readers to 
remember that the FOM is a statistical quantity: we have a probability 
distribution for the true phase, we pick one phase (the "centroid" 
phase that should minimise the RMS error in the density map), and then 
the FOM is the expected value of the phase error, obtained by taking 
the cosines of all possible phase differences and weighting by the 
probability of that phase difference.  Because it's a statistical 
quantity from a random distribution, you really can't expect this to 
agree reflection by reflection!  It's a good start to see that the 
overall values are good, but if you want to look more closely you have 
to look a groups of reflections, e.g. bins of resolution, bins of 
observed amplitude, bins of calculated amplitude.  However, each bin 
has to have enough members that the average will generally be close to 
the expected value.


Best wishes,

Randy Read

On 4 Oct 2019, at 16:38, James Holton > wrote:


I've done a few little experiments over the years using simulated 
data where I know the "correct" phase, trying to see just how 
accurate FOMs are.  What I have found in general is that overall FOM 
values are fairly well correlated to overall phase error, but if you 
go reflection-by-reflection they are terrible.  I suppose this is 
because FOM estimates are rooted in amplitudes. Good agreement in 
amplitude gives you more confidence in the model (and therefore the 
phases), but if your R factor is 55% then your phases probably aren't 
very good either.  However, if you look at any given h,k,l those 
assumptions become less and less applicable.  Still, it's the only 
thing we've got.


2qwAt the end of the day, the phase you get out of a refinement 
program is the phase of the model.  All those fancy "FWT" 
coefficients with "m" and "D" or "FOM" weights are modifications to 
the amplitudes, not the phases.  The phases in your 2mFo-DFc map are 
identical to those of just an Fc map.  Seriously, have a look! 
Sometimes you will get a 180 flip to keep the sign of the amplitude 
positive, but that's it.  Nevertheless, the electron density of a 
2mFo-DFc map is closer to the "correct" electron density than any 
other map.  This is quite remarkable considering that the "phase 
error" is the same.


This realization is what led my colleagues and I to forget about 
"phase error" and start looking at the error in the electron density 
itself (10.1073/pnas.1302823110).  We did this rather pedagogically.  
Basically, pretend you did the whole experiment again, but "change 
up" the source of error of interest.  For example if you want to see 
the effect of sigma(F) then you add random noise with the same 
magnitude as sigma(F) to the Fs, and then re-refine the structure.  
This gives you your new phases, and a new map. Do this 50 or so times 
and you get a pretty good idea of how any  source of error of 
interest propagates into your map.  There is even a little feature in 
coot for animating these maps, which gives a much more intuitive view 
of the "noise".  You can also look at variation of model parameters 
like the refined occupancy of a ligand, which is a good way to put an 
"error bar" on it.  The trick is finding the right 

Re: [ccp4bb] Issues in new Mac version 10.15

[William G. Scott]

 

Which ones? 

All of the binaries in $CBIN I have say "Mach-O 64-bit executable x86_64”  So 
that is unlikely the issue.

I haven’t installed Catalina yet, as I only have one computer that is new 
enough.  But one of the changes is they have locked down much of the file 
system, and are urging installation into /opt  (which is where X11 now gets 
installed, for example).

I have CCP4 installed in /opt/xtal/ccp4-7.0

You can do this with the tarball and manual install.

I’m going to help a student here with this today.  I’ll report back if it works.

Also, reinstallation of X11 is probably a good idea.

Sorry BTW to everyone for not keeping the Crystallography on OS X website more 
up to date.  I will try to do so shortly.  (The morale-sappers here finally got 
to me.)

Peace and joy,

Bill





> On Oct 16, 2019, at 12:44 AM, Ruud Hovius  wrote:
> 
> Hello, 
> 
> this is the warning that our IT people gave us :
> 
> 
> "Do not install the MAcOS upgrade to the new system CATALINA
> 
> This system version will apparently NOT allow 32-bit applications to run, 
> which are still many , 
> see https://support.apple.com/en-us/HT208436
> 
> 
> Try to go back to the former MacOS
> 
> A+
> 
> Ruud
> 
> On 16/10/19 01:50, Werther, Rachel A wrote:
>> 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 / 
>> 206-667-4066
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
> 
> -- 
> 
> Ruud Hovius
> EPFL SB ISIC LCBM 
> Office CH B3 424
> CH-1015 Lausanne
> mobile : +41 79 435 34 73 
> office : +41-21-693-3134
> 
> http://people.epfl.ch/ruud.hovius
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] LAST CHANCE: DLS/CCP4 data analysis workshop 2019

[David Waterman]

Dear all,

Please note the application period for this year's DLS/CCP4 workshop
closes *this
Friday*.

Best wishes
-- David


-- Forwarded message -
From: David Waterman 
Date: Tue, 1 Oct 2019 at 15:30
Subject: DLS/CCP4 data analysis workshop 2019
To: 


PhD students, postdocs and early career scientists,

Please consider applying for the sixth joint DLS/CCP4 workshop on MX data
collection and structure solution, to be held at Diamond Light Source, UK
from the 1st to the 8th December 2019.

This course offers the opportunity for you to work alongside leaders in the
field of MX on data from your own crystals. For more details please check
here:

http://www.ccp4.ac.uk/schools/DLS-2019/

The workshop has been very successful in previous years, as shown by
acknowledgements given in publications from attendees of the course:

http://www.ccp4.ac.uk/schools/DLS-school/index.php

The application period is now open and will* close on the 18th October*.
Applicants will be required to submit a CV/resume, describe their projects
and obtain a letter of support from a supervisor, so please do not wait
until the last minute to apply! Those with crystals and/or data will be
given priority.

Best wishes on behalf of the organisers,

David Waterman (CCP4)



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Issues in new Mac version 10.15

[Ruud Hovius]

Hello,

this is the warning that our IT people gave us :


*"Do not *install the MAcOS upgrade to the new system CATALINA

This system version will apparently NOT allow 32-bit applications to 
run, which are still many ,

see https://support.apple.com/en-us/HT208436


Try to go back to the former MacOS

A+

Ruud

On 16/10/19 01:50, Werther, Rachel A wrote:


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  / 206-667-4066





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



--

Ruud Hovius
EPFL SB ISIC LCBM
Office CH B3 424
CH-1015 Lausanne
mobile : +41 79 435 34 73
office : +41-21-693-3134
http://people.epfl.ch/ruud.hovius




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1