Re: [ccp4bb] Figure of merit in refinement

[Keller, Jacob]

>>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 ..

Could we add that all crystals are twinned, just some are in such a way as to 
be a problem?

JPK


On Wed, Oct 16, 2019 at 6:24 PM Randy Read 
mailto:rj...@cam.ac.uk>> 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 
mailto:jmhol...@lbl.gov>> 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. 

[ccp4bb] Call for Stanford-SLAC Cryo-EM Center (S2C2) Applications: Deadline November 1, 2019

[Dunn, Lisa B.]

Dear All,

The next deadline for submitting proposals to the Stanford-SLAC Cryo-EM Center 
(S2C2) is November 1, 2019.

 The missions of the Stanford-SLAC Cryo-EM Center (S2C2) are:

  1.  to provide access to state-of-the-art cryo-EM instruments for data 
collection towards atomic resolution structure determination of biochemically 
purified single particles
  2.  to enable scientists across the nation to become independent cryo-EM 
investigators
More information about the S2C2 program and the project application process is 
available at:  https://cryoem.slac.stanford.edu/s2c2/.Register in the user 
portal at https://userportal.slac.stanford.edu/ to submit your proposal.

Best regards,

Lisa Dunn
Stanford-SLAC Cryo-EM Center (S2C2)
SLAC National Accelerator Laboratory
2575 Sand Hill Rd.
Menlo Park, CA 94025
l...@slac.stanford.edu




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

[ccp4bb] Job opening: Scientist-I (Structural Biology) at Frederick National Laboratory for Cancer Research

[Dhirendra K Simanshu]

Hello everyone,

The Frederick National Laboratory for Cancer Research is looking for a
Scientist with experience in protein chemistry and structural biology. The
candidate will join the structural biology group within the NCI RAS
Initiative program and work on the protein-small molecule complexes.

For detailed information and to apply for this position, please use this
link:
https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4=leidosbiomed=765

Best regards
Dhirendra Simanshu


--

Dhirendra Simanshu

Principal Scientist, Team Lead - RAS Structural Biology

NCI RAS Initiative

Frederick National Laboratory for Cancer Research

Leidos Biomedical Research, Inc.

*Office/Courier*: 8560 Progress Drive, C1012, Frederick, MD 21701

*USPS mail*: Post Office Box B, ATRF-C1012, Frederick, MD 21702

dhirendra.siman...@fnlcr.nih.gov 



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

[ccp4bb] Job opening: Scientist, NMR/Structural Biology

[Ying Zhang]

Dear all,
  This post is to bring your attention to a job opportunity of a scientist 
position at Plexxikon Inc.  We are looking for a highly motivated, structural 
biologist with expertise in NMR.  Please help to distribute this to anyone that 
might be interested.  Plexxikion is located in Berkeley at CA, USA.  We only 
consider candidates based in US.
 This Scientist will be a critical member of the Structural Chemistry team 
reporting to the Associate Director.  This is an exceptional opportunity to 
gain experience in structure-guided drug discovery in a successful biotech 
company.
   Plexxikon utilizes its proprietary discovery platform to successfully 
develop a portfolio of competitively differentiated clinical and preclinical 
stage compounds in a number of therapeutic areas, including two marketed drug. 
Zelboraf(tm) (vemurafenib) was the first precision medicine to be approved for 
the treatment of BRAF-mutant metastatic melanoma; Turalio(tm) (pexidartinib) 
was the first FDA-approved therapy for tenosynovial giant cell tumor.

 You can find details about this position at 
https://careers.jobscore.com/careers/plexxikon/jobs/scientist-nmr-structural-biology-aCqwCO8cGr6BptaKiznY58
Please apply through the link.

  Best Regards,
Ying Zhang, Ph.D
Head of Structural Chemistry.
Plexxikon Inc





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

[Charles Ballard - UKRI STFC]

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/,
 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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of "Werther, Rachel A" 
mailto:rwert...@fredhutch.org>>
Reply-To: "Werther, Rachel A" 
mailto:rwert...@fredhutch.org>>
Date: Tuesday, October 15, 2019 at 5:01 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
mailto: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




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

[Jan Dohnalek]

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 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 

[ccp4bb] RFP for Small Molecule Discovery - AIMS Awards Deadline is October 28th

[Nick DeHaan]

Hi CCP4BB,

The application deadline for the AIMS Awards program is less than two weeks
away!

For anyone with a solved protein structure, an AIMS Award can help you
discover new small molecule binders. The program is open to investigators,
postdocs, and graduate students worldwide.

Applications are short (~30mins), and >300 awards will be given out this
cycle. Please reach out if you have any questions!

*Learn More*
Website: www.atomwise.com/aims 
Infographic:
http://www.atomwise.com/wp-content/uploads/2019/10/AIMS-Infographic-Stats_Fall2019.jpg

Flyer:
http://www.atomwise.com/wp-content/uploads/2019/10/Atomwise-AIMS-Awards-Flyer-Fall-2019_updated-1.pdf


Best regards,
Nick


Nick DeHaan, MsE
*Partnering Executive*
*Atomwise*  | *Better Medicines Faster*
ᐧ

-- 
Confidentiality Notice: The information contained herein is for 
informational purposes only. This message is private and the information 
contained in this message, including any attachments, contains information 
that may be confidential, privileged and/or proprietary. It is intended to 
be read only by the individual or entity to whom it is addressed. If you 
are not the intended recipient, please notify the sender by replying to 
this message, delete the material immediately from your system and note 
that you must not review, disclose, copy, distribute or take any action in 
reliance on or in reference to this message, including any attachments.  No 
confidentiality, privilege, or property rights are waived or lost by any 
errors in transmission. Any unauthorized use or disclosure of the contents 
of this message is not permitted and may be unlawful.



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