Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

[Billy Poon]

Hi all,

When opening Coot from ccp4 8 in Phenix, there may be an issue with the
restraints since some environment variables may not be set. The terminal
should show something like

/Applications/ccp4-8.0/coot_py2/bin/coot: line 81:
/Applications/ccp4-8.0/coot_py2/bin/ccp4.setup-sh: No such file or
directory
WARNING:: Coot REFMAC dictionary override COOT_REFMAC_LIB_DIRfailed to find
a dictionary /Applications/ccp4-8.0/coot_py2/share/coot/lib
WARNING:: COOT_PREFIX set, but no dictionary lib found

WARNING: Failed to read restraints dictionary.

WARNING: in init_refmac_mon_lib, file
"/data/monomers/list/mon_lib_list.cif" not found.

WARNING: file /data/monomers/a/ALA.cif is not a regular file
...

One workaround that should work is to make a symbolic link of the
ccp4-8.0/bin/ccp4.setup-sh file in ccp4-8.0/bin/ccp4/coot_py2/bin. You
should then see that Coot loads restraints

INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
/Applications/ccp4-8.0/lib/data/monomers/
There are 223 data in
/Applications/ccp4-8.0/lib/data/monomers/list/mon_lib_list.cif

There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/a/ALA.cif
...

Alternatively, you can also source the ccp4-8.0/bin/ccp4.setup-sh file
before starting Phenix, or manually set CLIBD_MON. Then, the necessary
environment variable is set.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Fax: (510) 486-5909
Web: https://phenix-online.org


On Tue, Jul 26, 2022 at 7:17 PM Paul Emsley 
wrote:

> On 27/07/2022 01:44, Dale C wrote:
> > Hi all,
> >
> > I recently updated my ccp4 package to Program suite v8.0.002 and i have
> now run into a few issues with other programs. The issues are highlighted
> below...
> >
> > - When i click 'Open in Coot' on any output through Phenix (so far only
> tested phenix.refine and phenix.phaser), i no longer see anything open. Nor
> do i see the "Connected to Phenix" button in the toolbar on Coot.
> There is probably useful information written to the terminal. AFAIR, you
> are not the first person to experience this, I forget what the problem
> and solution was but I think that it was trivial.
> >
> > - Coot also seems to have an issue with not loading the amino acid
> restraints so when i click real-space refine, i get the error 'unable to
> find restraints for residue x,y,z'.
> >
> When you start Coot, what does it say as it tries to load the
> dictionaries for the standard residues?
>
> Paul.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

[Paul Emsley]

On 27/07/2022 01:44, Dale C wrote:

Hi all,

I recently updated my ccp4 package to Program suite v8.0.002 and i have now run 
into a few issues with other programs. The issues are highlighted below...

- When i click 'Open in Coot' on any output through Phenix (so far only tested 
phenix.refine and phenix.phaser), i no longer see anything open. Nor do i see the 
"Connected to Phenix" button in the toolbar on Coot.
There is probably useful information written to the terminal. AFAIR, you 
are not the first person to experience this, I forget what the problem 
and solution was but I think that it was trivial.


- Coot also seems to have an issue with not loading the amino acid restraints 
so when i click real-space refine, i get the error 'unable to find restraints 
for residue x,y,z'.

When you start Coot, what does it say as it tries to load the 
dictionaries for the standard residues?


Paul.



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Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

[Dale Calleja]

Ah yes, thank you.

MacOS Moneterey v12.4.

Dale.

Dale Calleja
PhD Student, Komander Lab
Ubiquitin Signalling Division

WEHI
1G Royal Parade
Parkville  VIC  3052
Australia
Email callej...@wehi.edu.au

From: Joel Tyndall 
Date: Wednesday, 27 July 2022 at 11:19 am
To: Dale Calleja , CCP4BB@JISCMAIL.AC.UK 

Subject: RE: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8
PC, mac or linux?

-Original Message-
From: CCP4 bulletin board  On Behalf Of Dale C
Sent: Wednesday, 27 July 2022 12:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

Hi all,

I recently updated my ccp4 package to Program suite v8.0.002 and i have now run 
into a few issues with other programs. The issues are highlighted below...

- When i click 'Open in Coot' on any output through Phenix (so far only tested 
phenix.refine and phenix.phaser), i no longer see anything open. Nor do i see 
the "Connected to Phenix" button in the toolbar on Coot.

- The 'fetch' command in Pymol no longer works either (I have attached a 
screenshot of the error message here)

- Coot also seems to have an issue with not loading the amino acid restraints 
so when i click real-space refine, i get the error 'unable to find restraints 
for residue x,y,z'.

I feel they may be all related and my first thought is that it has something to 
do with my Python dependencies however I have no idea how to fix this or 
reinstall them.

Does anyone have an idea if they are all related? Or how i might fix this?

fyi I am using
- ccp4 program suit v8.0.002
- Coot 0.9.8.3
- Phenix-1.20.1-4487

Thanks in advance.

Dale.





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Re: [ccp4bb] [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

[Dale Calleja]

Hi Blaine,

Thanks for your reply, I thought maybe this was related to my issue with ccp4, 
though I’ll also direct this to the PyMol mailing list as you suggested.

I am currently using version 2.5.0, unfortunately neither type=pdb or type =cif 
seemed to fix the issue ☹

Dale.

Dale Calleja
PhD Student, Komander Lab
Ubiquitin Signalling Division

WEHI
1G Royal Parade
Parkville  VIC  3052
Australia
Email callej...@wehi.edu.au

From: Mooers, Blaine H.M. (HSC) 
Date: Wednesday, 27 July 2022 at 12:04 pm
To: CCP4BB@JISCMAIL.AC.UK , Dale Calleja 

Subject: Re: [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing 
ccp4 v8
Hi Dale,

Which version of PyMOL are you using?
(PyMOL questions should really be directed to the PyMOL mailing list).
Ancient versions of PyMOL may not accept cif files via fetch unless you include 
the type=cif​ keyword.
To get the pdb file downloaded, try fetch 6wrh type=pdb​.
I can download 6wrh into a recent incentive version of PyMOL (2.5.2) via fetch 
6wrh​.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: 
https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): 
https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology

From: CCP4 bulletin board  on behalf of Dale C 
<8378c932659c-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, July 26, 2022 7:44 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 
v8

Hi all,

I recently updated my ccp4 package to Program suite v8.0.002 and i have now run 
into a few issues with other programs. The issues are highlighted below...

- When i click 'Open in Coot' on any output through Phenix (so far only tested 
phenix.refine and phenix.phaser), i no longer see anything open. Nor do i see 
the "Connected to Phenix" button in the toolbar on Coot.

- The 'fetch' command in Pymol no longer works either (I have attached a 
screenshot of the error message here)

- Coot also seems to have an issue with not loading the amino acid restraints 
so when i click real-space refine, i get the error 'unable to find restraints 
for residue x,y,z'.

I feel they may be all related and my first thought is that it has something to 
do with my Python dependencies however I have no idea how to fix this or 
reinstall them.

Does anyone have an idea if they are all related? Or how i might fix this?

fyi I am using
- ccp4 program suit v8.0.002
- Coot 0.9.8.3
- Phenix-1.20.1-4487

Thanks in advance.

Dale.





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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

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Re: [ccp4bb] [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

[Mooers, Blaine H.M. (HSC)]

Hi Dale,

Which version of PyMOL are you using?
(PyMOL questions should really be directed to the PyMOL mailing list).
Ancient versions of PyMOL may not accept cif files via fetch unless you include 
the type=cif​ keyword.
To get the pdb file downloaded, try fetch 6wrh type=pdb​.
I can download 6wrh into a recent incentive version of PyMOL (2.5.2) via fetch 
6wrh​.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: 
https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): 
https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology

From: CCP4 bulletin board  on behalf of Dale C 
<8378c932659c-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, July 26, 2022 7:44 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 
v8

Hi all,

I recently updated my ccp4 package to Program suite v8.0.002 and i have now run 
into a few issues with other programs. The issues are highlighted below...

- When i click 'Open in Coot' on any output through Phenix (so far only tested 
phenix.refine and phenix.phaser), i no longer see anything open. Nor do i see 
the "Connected to Phenix" button in the toolbar on Coot.

- The 'fetch' command in Pymol no longer works either (I have attached a 
screenshot of the error message here)

- Coot also seems to have an issue with not loading the amino acid restraints 
so when i click real-space refine, i get the error 'unable to find restraints 
for residue x,y,z'.

I feel they may be all related and my first thought is that it has something to 
do with my Python dependencies however I have no idea how to fix this or 
reinstall them.

Does anyone have an idea if they are all related? Or how i might fix this?

fyi I am using
- ccp4 program suit v8.0.002
- Coot 0.9.8.3
- Phenix-1.20.1-4487

Thanks in advance.

Dale.





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Re: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

[Joel Tyndall]

PC, mac or linux?

-Original Message-
From: CCP4 bulletin board  On Behalf Of Dale C
Sent: Wednesday, 27 July 2022 12:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

Hi all,

I recently updated my ccp4 package to Program suite v8.0.002 and i have now run 
into a few issues with other programs. The issues are highlighted below...

- When i click 'Open in Coot' on any output through Phenix (so far only tested 
phenix.refine and phenix.phaser), i no longer see anything open. Nor do i see 
the "Connected to Phenix" button in the toolbar on Coot.

- The 'fetch' command in Pymol no longer works either (I have attached a 
screenshot of the error message here)

- Coot also seems to have an issue with not loading the amino acid restraints 
so when i click real-space refine, i get the error 'unable to find restraints 
for residue x,y,z'.

I feel they may be all related and my first thought is that it has something to 
do with my Python dependencies however I have no idea how to fix this or 
reinstall them.

Does anyone have an idea if they are all related? Or how i might fix this?

fyi I am using
- ccp4 program suit v8.0.002
- Coot 0.9.8.3
- Phenix-1.20.1-4487

Thanks in advance.

Dale.





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[ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

[Dale C]

Hi all,

I recently updated my ccp4 package to Program suite v8.0.002 and i have now run 
into a few issues with other programs. The issues are highlighted below...

- When i click 'Open in Coot' on any output through Phenix (so far only tested 
phenix.refine and phenix.phaser), i no longer see anything open. Nor do i see 
the "Connected to Phenix" button in the toolbar on Coot.

- The 'fetch' command in Pymol no longer works either (I have attached a 
screenshot of the error message here)

- Coot also seems to have an issue with not loading the amino acid restraints 
so when i click real-space refine, i get the error 'unable to find restraints 
for residue x,y,z'.

I feel they may be all related and my first thought is that it has something to 
do with my Python dependencies however I have no idea how to fix this or 
reinstall them.

Does anyone have an idea if they are all related? Or how i might fix this?

fyi I am using
- ccp4 program suit v8.0.002
- Coot 0.9.8.3
- Phenix-1.20.1-4487

Thanks in advance.

Dale.





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[ccp4bb] Postdoctoral position at ICTER in Warsaw, Poland -– final warning

[Humberto Fernandes]

Dear all

This is a final reminder for this post. The closing date is the 27th of July.

A postdoctoral position in the Integrated Structural Biology lab at The 
International Center for Translational Eye Research (ICTER) in Warsaw, Poland, 
is available for highly motivated biologists, biochemists, or structural 
biologists, funded until the end of 2023. The position involves cloning, 
protein production, purification, characterization, and structural elucidation 
of proteins of the phototransduction pathway.

For details and how to apply, until the 27th of July, see:
https://icter.pl/jobs/junior-postdoctoral-researcher-in-structural-biology/

Feel free to spread this information at your institutes and to interested 
colleagues. And please do not hesitate to contact me if you have any questions.

Thank you, and have a great day,

Humberto



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Re: [ccp4bb] symmetry possibilities

[Jorge Iulek]

Thanks Eleanor.

We tried to educate our crystals, through better purification and 
crystallization refinement, we got progress, but not enough to get 
totally well behaved ones.


Yes, even at P212121, plot from pointless indicates, at least partial, 
twinning.


Overlapping reflections, we did get at our first Synchrotron data 
collection and certainly many of the intensity values there are 
contaminated by (non-merohedral - pseudo or not - twinning ) overlap; at 
the second collection, there is no obvious sight of this eyeballing the 
images and even the data processing program did not indicated any 
severity on this.


Yours,


Jorge


eleanorOh dear - why don’t crystals behave better!

Re twinning - do the data processing Plots indicate twinning?  ( L 
test?2nd moments?)


It sounds rather more like overlapping diffraction where only some of 
the observations are Affected.


Eleanor

On Thu, 21 Jul 2022 at 10:50, Flaig, Ralf (DLSLtd,RAL,LSCI) 
<8308ad6ea74c-dmarc-requ...@jiscmail.ac.uk 
> wrote:


This paper by Pietro Roversi might help:

https://journals.iucr.org/d/issues/2012/04/00/ba5182/index.html



Kind regards,
Ralf

-Original Message-
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Kay Diederichs
Sent: 20 July 2022 22:11
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] symmetry possibilities

Dear Jorge,

what you write makes sense to me, and I cannot answer your
questions. This is just to say that the situation you encounter is
not completely uncommon, although most crystallographers would
abandon such a crystal form, I guess.
The technical term that describes this 4-fold twinning is
"tetartohedral twinning" (in contrast to merohedral twinning,
which involves two twin domains); maybe this helps to find
additional pointers.

best wishes,
Kay

On Wed, 20 Jul 2022 11:10:04 -0300, Jorge Iulek mailto:jiu...@gmail.com>> wrote:

>Dear all,
>
>
>  We had some data collections at a Synchrotron. Crystals are a
>kind of brush like (lattice strains, to use a term by Dr. Bergfors,
>though we employed good effort for purification), but we took
advantage
>of the Synchrotron microfocus.
>
>     Some of the datasets (images) clearly shows more than one
lattice
>(maybe more than two) that, struggling, we managed to process a
get a
>dataset which allowed molecular replacement and then (initial)
refinement.
>
>     But, in a second Synchrotron travel (and after efforts for
>improving crystals), we got in some cases images with spots "well
>separated'  "unique lattice" at some of the target spots
(radiation on
>the crystal) in the crystal.
>
>     We processed these happily to P212121 (though some strange
points
>by pointless and/or xtriage, namely that " the L-test suggests
that the
>data may be twinned,  so the indicated Laue symmetry may be too
high").
>Systematic absences seem to be OK for lower resolution
reflections, but
>at higher resolution there seems to be more of a modulation (if a
look
>at a P222 processing).
>
>     Anyway, we took, initially, refinement at P212121,
nevertheless (I
>should say not surprisingly), it stuck at 30/31 % R-free, model
close
>(if not at all) to completion. Data resolution is 2.31 A.
>
>     We went to process these images in P1, and in the three possible
>P21  (named P21_45, P21_122 and P21_155 - according to approx. axis
>dimensions) sg's. Then we went to refine (refmac, twin option) the
>current model (and then due "symmetry copies" produced with
pdbset and
>added to the model to be refined,) in all possible space groups, and
>*care was taken* to  inherit the former r-free set *and* make the
then
>corresponding twin related reflections to be in the r-free set
(to be
>close to 5% of reflections, but "independent" reflections). It
turned
>out that the R/Rfree values dropped around to ~19/25% for P1 and one
>(namely, P21_b151) of the P21; higher values for other P21's. As
>expected, twin domains refine more or less close to 25 (P1) and 50%
>(any P21), respectively.
>
>     To mess up a bit more, I made the same study with "another
dataset"
>(another illuminated spot on the - same - crystal). In this case,
only
>the dataset processed in P1 presented "good" R values.
>
>     I think these observations might correlate to what the
"crystal "
>physically is... a mix of portions genuinely P212121 but mixed,
more or
>less, that in some places with twins in one or more other types,
>depending on where I focus my beam.
>
>     Should 

Re: [ccp4bb] symmetry possibilities

[Jorge Iulek]

Dear Ben,



Hi Jorge,
   I have had some similar cases.
The twin fraction can vary during data collection on the synchrotron 
(different areas of the crystal can have different twin fractions).


    Yes, Ben, this seems perfectly feasible to me. But your observation 
prompted me to think about radiation damaged and if this could also lead 
to symmetry "distortion/loss" during data collection. We have the 
experimental data in hands and hope to have tools to deal with them 
correctly, but we also want to know what the reality is behind the 
behavior we observe.



Sometimes this is not a problem and twin refinement works fine -
    We have initial observations that point to a good work with twin 
refinement. Most of the structure seems to have good electron density at P1.
sometimes it is a problem and it is hard to get a clear 
electron density map from the structure.
 R-factors from twinned structures tend to be lower than 'normal' 
R-factors - your ~19/25% would be OK for normal data but ...
If the twin fraction varies as you rotate the crystal and illuminate 
different volumes you can sometimes select fewer images to help.


    That is something we will consider, but for while we will see where 
advancing with P1 from the 3600 images goes to!


    Thanks,


Jorge




Kind regards, Ben

On Wed, Jul 20, 2022 at 10:12 PM Kay Diederichs 
> wrote:


Dear Jorge,

what you write makes sense to me, and I cannot answer your
questions. This is just to say that the situation you encounter is
not completely uncommon, although most crystallographers would
abandon such a crystal form, I guess.
The technical term that describes this 4-fold twinning is
"tetartohedral twinning" (in contrast to merohedral twinning,
which involves two twin domains); maybe this helps to find
additional pointers.

best wishes,
Kay

On Wed, 20 Jul 2022 11:10:04 -0300, Jorge Iulek mailto:jiu...@gmail.com>> wrote:

>Dear all,
>
>
>  We had some data collections at a Synchrotron. Crystals are
a kind
>of brush like (lattice strains, to use a term by Dr. Bergfors,
though we
>employed good effort for purification), but we took advantage of the
>Synchrotron microfocus.
>
>     Some of the datasets (images) clearly shows more than one
lattice
>(maybe more than two) that, struggling, we managed to process a get a
>dataset which allowed molecular replacement and then (initial)
refinement.
>
>     But, in a second Synchrotron travel (and after efforts for
>improving crystals), we got in some cases images with spots "well
>separated'  "unique lattice" at some of the target spots
(radiation on
>the crystal) in the crystal.
>
>     We processed these happily to P212121 (though some strange
points
>by pointless and/or xtriage, namely that " the L-test suggests
that the
>data may be twinned,  so the indicated Laue symmetry may be too
high").
>Systematic absences seem to be OK for lower resolution
reflections, but
>at higher resolution there seems to be more of a modulation (if a
look
>at a P222 processing).
>
>     Anyway, we took, initially, refinement at P212121,
nevertheless (I
>should say not surprisingly), it stuck at 30/31 % R-free, model close
>(if not at all) to completion. Data resolution is 2.31 A.
>
>     We went to process these images in P1, and in the three possible
>P21  (named P21_45, P21_122 and P21_155 - according to approx. axis
>dimensions) sg's. Then we went to refine (refmac, twin option) the
>current model (and then due "symmetry copies" produced with
pdbset and
>added to the model to be refined,) in all possible space groups, and
>*care was taken* to  inherit the former r-free set *and* make the
then
>corresponding twin related reflections to be in the r-free set (to be
>close to 5% of reflections, but "independent" reflections). It turned
>out that the R/Rfree values dropped around to ~19/25% for P1 and one
>(namely, P21_b151) of the P21; higher values for other P21's. As
>expected, twin domains refine more or less close to 25 (P1) and
50% (any
>P21), respectively.
>
>     To mess up a bit more, I made the same study with "another
dataset"
>(another illuminated spot on the - same - crystal). In this case,
only
>the dataset processed in P1 presented "good" R values.
>
>     I think these observations might correlate to what the
"crystal "
>physically is... a mix of portions genuinely P212121 but mixed,
more or
>less, that in some places with twins in one or more other types,
>depending on where I focus my beam.
>
>     Should I look at anything else to establish twin P1 is the
best way
>to refine this structure?
>
>
>     Related, and a question I me

Re: [ccp4bb] symmetry possibilities

[Jorge Iulek]

Dear Dom.


    Yes, Zanuda must also give more insights, well pointed (it goes 
straight to my question "Should I look at anything else to establish 
twin P1 is the best way to refine this structure?"). By the way, though 
we have not gone through P1 in/extensively for while, a brief overview 
has indicate some (new, but few, for while) side chains that, although 
not all that ordered, must have preferential conformations.


    Yours,


J.


On 7/23/22 5:55 AM, Dom Bellini wrote:

Hi Jorge,

Should I look at anything else to establish twin P1 is the best way 
to refine this structure?
You could feed your refined model and map coefficients to Zanuda (CCP4 
program) which automatically will check which higher symmetry space 
group will give lower Rfactors in refinement, pointing to real crys 
symmetry (similarly to what you have been doing manually).


Good luck!

D




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Re: [ccp4bb] symmetry possibilities

[Jorge Iulek]

Thank you, Edward, for sharing this. I will read through the (extensive) 
details of the work.



J.


On 7/22/22 10:25 PM, Edward A. Berry wrote:
As for your second question, whether refining in a lower symmetry 
affects the R-factors,


On 7/20/22 10:10 AM, Jorge Iulek wrote:
 Related, and a question I mentioned before in this forum: what 
if a genuine 2 axis (say , P222 to P2, or even to P1) (I do not mean 
this is the case here) is ignored such that one would have doubled 
the number of observations but also doubled the number of parameters 
to be refined (suppose to exclude NCS in any case). Would one expect 
R/Rfree values to be similar in both P222 and P2 (or even P1)? How 
much extra freedom would one have besides the twin domain fractions 
to refine?



The experiment described here:
  https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg46635.html
addresses this, although it wasn't the main point of that email.

The structures 1CHR and 2CHR are derived from the same crystal. Data 
was collected in I4 and 1CHR was published with this space group, and 
with the low symmetry data.  It was later concluded that the true 
space group was I422. The original data was reduced to that space 
group and the structure solved again. In the experiment described in 
the email referenced above, the model of 2chr was refined using (then) 
current phenix.refine. In parallel the 2CHR structure was expanded to 
a dimer and refined against the original low-symmetry data.


Because the number of reflections was low (even with 10% free) the 
uncertainty in R-free was high, so the refinement was repeated 10 
times in each case, with different randomly selected free sets, to get 
the average. In each case the refinement was carried out for 50 
macrocycles to approach convergence. The R and Free-R values were not 
significantly different.

eab

From that email:
2. The deposited structure was refined in I422 10 times, 50 macrocycles
each, with randomly picked 10% free reflections
 R: 0.1725±0.0013   Rfree: 0.2507±0.0062  Nfree: 908.9±   Nrefl: 9087

3. The structure was expanded to an I4 dimer related by the unused I422
crystallographic operator, matching the dimer of 1chr. This dimer was
refined against the original (I4) data of 1chr, picking free reflections
in symmetry related pairs. This was repeated 10 times with different
random seed for picking reflections.
R: 0.1666±0.0012   **Rfree:0.2523±0.0077   Nfree: 1601.4 Nrefl:16011

4. same as 3 but picking free reflections randomly without regard for
lattice symmetry.
On average 15 free reflections were in pairs, 212 were invariant under
the operator (no sym-mate) and 1374 (86%) were paired with working
reflections.
R: 0.1674±0.0017   **Rfree:0.2523±0.0050  Nfree: 1600.9 Nrefl:16011




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Re: [ccp4bb] Comparing two datasets

[Cygler, Miroslaw]

Thank you all for your answers and suggestions. Pointless got the data I wanted.

Mirek




On Jul 26, 2022, at 9:09 AM, Clemens Vonrhein 
mailto:vonrh...@globalphasing.com>> wrote:

CAUTION: External to USask. Verify sender and use caution with links and 
attachments. Forward suspicious emails to 
phish...@usask.ca


Dear all,

[just to add some caveats in case future students see this thread and
start cut-n-pasting commands to successfully create some kind of MTZ
file of dubious content]

Unless we're talking about some really old datasets (of historical
interest) or a disastrous situation (all backups lost), by far the
best approach would be to go back to the original data in the form of
the (unscaled) unmerged intensities - in order to do the
scaling+merging of the two datasets then, right?

One can do all kind of things with amplitudes (F) in MTZ files using
various fabulous CCP4 programs (SFTOOLS, SCALEIT, RSTATS, CAD,
POINTLESS, COMBAT), but be careful that it is not just some
simple/brainless arithmetic on numerical values that happen to be
called F/SIGF. Been there, done that, got the T-shirt ...

The important thing is to understand what the OP is trying to achive
here. As others mentioned:

 ... calculate R-merge for Fs from two datasets processed from two
 different crystals ...

sounds to like a confusion between

(1) comparing two sets of amplitudes via an R-factor (not R-merge!)

* can be done with e.g. SCALEIT or RSTATS

* with or without scaling?

* what scale parametrisation (k, k/B, anisotropic)?

* overall or in bins? What binning?

(2) getting a "R-merge" value for some kind of "Table-1" (paper or
deposition):

* can't be done "correctly" from amplitudes

* go back to original data and (re)processing

And

 ... would take two mtz files and merge the Fs ...

might just ask for a method to "average" two sets of amplitudes:

 * inverse-variance weighted?

 * unweighted?

 * for what purpose - and why not go back to the original data to do
   proper scaling/merging there?

The subject line "Comparing two datasets" seems to ask for something
different again: a way of comparing (R-factor? CC?) datasets, not
necessarily combining/merging them?

Cheers

Clemens


On Tue, Jul 26, 2022 at 02:11:17PM +0100, Phil Evans wrote:
If you want to merge them then you can use Pointless/Aimless/ctruncate, with 
the warning that the conversion from F to I is not ideal, and ctruncate should 
be set to regenerate F from I just as sqrt ie not apply the truncate procedure 
again.
Pointless supersedes combat for this conversion
Again, just for comparison use scaleit

Phil

Sent from my iPhone

On 26 Jul 2022, at 13:33, Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hello again, as far as I can tell, the question is about two already 
merged/unique datasets which Mirek wishes to merge into one. As far as I can 
tell/remember, Scaleit is for scaling datasets side-by-side to get isomorphous 
differences, etc, and I don't know of a way that you could get it to merge 2 
datasets as Mirek requested. Probably I am wrong but Scaleit R-factors are 
different from R-merge, although the latter might be a bit dubious in the 
circumstances. Anyway, I think the Combat route is a viable way of achieving 
what the questioner wants to achieve ;-0


Sent from ProtonMail mobile



 Original Message 
On 26 Jul 2022, 12:25, John R Helliwell < 
jrhelliw...@gmail.com> wrote:

Dear Colleagues,
Scaleit is a terrific program.
Amongst its strengths already listed I would also mention its breakdown table 
with F so that in the strongest F reflections bin any systematic errors between 
the two data sets can show up if the Rfactor is greater than about 1%.
Greetings,
John
Emeritus Professor John R Helliwell DSc




On 26 Jul 2022, at 11:40, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:


Not only does SCALEIT do the job - it presented useful plots and an informative 
log file..
Eleanor
(You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the 
columns from each Xtal will need different labels..)

On Tue, 26 Jul 2022 at 09:45, Phil Evans 
mailto:p...@mrc-lmb.cam.ac.uk>> wrote:
If you give Pointless Fs, it squares them to Is (not correct if the Fs have 
been derived from the truncate procedure, but not too bad). It will then give 
you a comparison. If you give the two datasets to Pointless, labelling them as 
different datasets, you can use Aimless to compare them

But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but still 
works and gives lots of statistics

Phil

Sent from my iPhone

On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB 
mailto:and...@mrc-lmb.cam.ac.uk>> wrote:

I think that POINTLESS works with intensities rather than structure factors

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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Comparing two datasets

[Jessica Bruhn]

Hi Mirek,

I have absolutely loved this discussion of other options for comparing
datasets! But to your original problem:

To tell CCP4 where r is installed, you need to add this to your $PATH. You
will want to figure out where r is installed on your computer and then add
it to your .bashrc file or .zshrc file if you are using a newer Mac. These
instructions might be helpful:
https://gist.github.com/nex3/c395b2f8fd4b02068be37c961301caa7 . You can
follow the instructions for Mac Os or for Linux.

You can tell that you have done this correctly by opening a new terminal
window and typing "which r" (no quotes) into the command prompt. It
should return a path to where you have r installed. You can then launch
ccp4 by typing "ccp4i2" into the command prompt. Clicking on the icon might
also work, but I generally launch CCP4 from a terminal window. Also, if you
have problems launching ccp4 from terminal, add this to your
.bashrc/.zshrc, making sure that the path you are listing is correct for
your installation of ccp4 and that you re-start your terminal after doing
this:

#ccp4

source /Applications/ccp4-7.1/bin/ccp4.setup-sh

Good luck!

Kind regards,
Jessica

On Tue, Jul 26, 2022 at 8:10 AM Clemens Vonrhein 
wrote:

> Dear all,
>
> [just to add some caveats in case future students see this thread and
> start cut-n-pasting commands to successfully create some kind of MTZ
> file of dubious content]
>
> Unless we're talking about some really old datasets (of historical
> interest) or a disastrous situation (all backups lost), by far the
> best approach would be to go back to the original data in the form of
> the (unscaled) unmerged intensities - in order to do the
> scaling+merging of the two datasets then, right?
>
> One can do all kind of things with amplitudes (F) in MTZ files using
> various fabulous CCP4 programs (SFTOOLS, SCALEIT, RSTATS, CAD,
> POINTLESS, COMBAT), but be careful that it is not just some
> simple/brainless arithmetic on numerical values that happen to be
> called F/SIGF. Been there, done that, got the T-shirt ...
>
> The important thing is to understand what the OP is trying to achive
> here. As others mentioned:
>
>   ... calculate R-merge for Fs from two datasets processed from two
>   different crystals ...
>
> sounds to like a confusion between
>
>  (1) comparing two sets of amplitudes via an R-factor (not R-merge!)
>
>  * can be done with e.g. SCALEIT or RSTATS
>
>  * with or without scaling?
>
>  * what scale parametrisation (k, k/B, anisotropic)?
>
>  * overall or in bins? What binning?
>
>  (2) getting a "R-merge" value for some kind of "Table-1" (paper or
>  deposition):
>
>  * can't be done "correctly" from amplitudes
>
>  * go back to original data and (re)processing
>
> And
>
>   ... would take two mtz files and merge the Fs ...
>
> might just ask for a method to "average" two sets of amplitudes:
>
>   * inverse-variance weighted?
>
>   * unweighted?
>
>   * for what purpose - and why not go back to the original data to do
> proper scaling/merging there?
>
> The subject line "Comparing two datasets" seems to ask for something
> different again: a way of comparing (R-factor? CC?) datasets, not
> necessarily combining/merging them?
>
> Cheers
>
> Clemens
>
>
> On Tue, Jul 26, 2022 at 02:11:17PM +0100, Phil Evans wrote:
> > If you want to merge them then you can use Pointless/Aimless/ctruncate,
> with the warning that the conversion from F to I is not ideal, and
> ctruncate should be set to regenerate F from I just as sqrt ie not apply
> the truncate procedure again.
> > Pointless supersedes combat for this conversion
> > Again, just for comparison use scaleit
> >
> > Phil
> >
> > Sent from my iPhone
> >
> > > On 26 Jul 2022, at 13:33, Jon Cooper <
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> > >
> > > Hello again, as far as I can tell, the question is about two already
> merged/unique datasets which Mirek wishes to merge into one. As far as I
> can tell/remember, Scaleit is for scaling datasets side-by-side to get
> isomorphous differences, etc, and I don't know of a way that you could get
> it to merge 2 datasets as Mirek requested. Probably I am wrong but Scaleit
> R-factors are different from R-merge, although the latter might be a bit
> dubious in the circumstances. Anyway, I think the Combat route is a viable
> way of achieving what the questioner wants to achieve ;-0
> > >
> > >
> > > Sent from ProtonMail mobile
> > >
> > >
> > >
> > >  Original Message 
> > > On 26 Jul 2022, 12:25, John R Helliwell < jrhelliw...@gmail.com>
> wrote:
> > >
> > > Dear Colleagues,
> > > Scaleit is a terrific program.
> > > Amongst its strengths already listed I would also mention its
> breakdown table with F so that in the strongest F reflections bin any
> systematic errors between the two data sets can show up if the Rfactor is
> greater than about 1%.
> > > Greetings,
> > > John
> > > Emeritus Professor John R Helliwell DSc
> > >
> 

Re: [ccp4bb] Comparing two datasets

[Clemens Vonrhein]

Dear all,

[just to add some caveats in case future students see this thread and
start cut-n-pasting commands to successfully create some kind of MTZ
file of dubious content]

Unless we're talking about some really old datasets (of historical
interest) or a disastrous situation (all backups lost), by far the
best approach would be to go back to the original data in the form of
the (unscaled) unmerged intensities - in order to do the
scaling+merging of the two datasets then, right?

One can do all kind of things with amplitudes (F) in MTZ files using
various fabulous CCP4 programs (SFTOOLS, SCALEIT, RSTATS, CAD,
POINTLESS, COMBAT), but be careful that it is not just some
simple/brainless arithmetic on numerical values that happen to be
called F/SIGF. Been there, done that, got the T-shirt ...

The important thing is to understand what the OP is trying to achive
here. As others mentioned:

  ... calculate R-merge for Fs from two datasets processed from two
  different crystals ...

sounds to like a confusion between

 (1) comparing two sets of amplitudes via an R-factor (not R-merge!)

 * can be done with e.g. SCALEIT or RSTATS

 * with or without scaling?

 * what scale parametrisation (k, k/B, anisotropic)?

 * overall or in bins? What binning?

 (2) getting a "R-merge" value for some kind of "Table-1" (paper or
 deposition):

 * can't be done "correctly" from amplitudes

 * go back to original data and (re)processing

And

  ... would take two mtz files and merge the Fs ...

might just ask for a method to "average" two sets of amplitudes:

  * inverse-variance weighted?

  * unweighted?

  * for what purpose - and why not go back to the original data to do
proper scaling/merging there?

The subject line "Comparing two datasets" seems to ask for something
different again: a way of comparing (R-factor? CC?) datasets, not
necessarily combining/merging them?

Cheers

Clemens


On Tue, Jul 26, 2022 at 02:11:17PM +0100, Phil Evans wrote:
> If you want to merge them then you can use Pointless/Aimless/ctruncate, with 
> the warning that the conversion from F to I is not ideal, and ctruncate 
> should be set to regenerate F from I just as sqrt ie not apply the truncate 
> procedure again. 
> Pointless supersedes combat for this conversion 
> Again, just for comparison use scaleit
> 
> Phil
> 
> Sent from my iPhone
> 
> > On 26 Jul 2022, at 13:33, Jon Cooper 
> > <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> > 
> > Hello again, as far as I can tell, the question is about two already 
> > merged/unique datasets which Mirek wishes to merge into one. As far as I 
> > can tell/remember, Scaleit is for scaling datasets side-by-side to get 
> > isomorphous differences, etc, and I don't know of a way that you could get 
> > it to merge 2 datasets as Mirek requested. Probably I am wrong but Scaleit 
> > R-factors are different from R-merge, although the latter might be a bit 
> > dubious in the circumstances. Anyway, I think the Combat route is a viable 
> > way of achieving what the questioner wants to achieve ;-0 
> > 
> > 
> > Sent from ProtonMail mobile
> > 
> > 
> > 
> >  Original Message 
> > On 26 Jul 2022, 12:25, John R Helliwell < jrhelliw...@gmail.com> wrote:
> > 
> > Dear Colleagues,
> > Scaleit is a terrific program. 
> > Amongst its strengths already listed I would also mention its breakdown 
> > table with F so that in the strongest F reflections bin any systematic 
> > errors between the two data sets can show up if the Rfactor is greater than 
> > about 1%. 
> > Greetings,
> > John 
> > Emeritus Professor John R Helliwell DSc
> > 
> > 
> > 
> > 
> >> On 26 Jul 2022, at 11:40, Eleanor Dodson 
> >> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> >> 
> >> 
> >> Not only does SCALEIT do the job - it presented useful plots and an 
> >> informative log file..
> >> Eleanor
> >> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously 
> >> the columns from each Xtal will need different labels..)
> >> 
> >> On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:
> >>> If you give Pointless Fs, it squares them to Is (not correct if the Fs 
> >>> have been derived from the truncate procedure, but not too bad). It will 
> >>> then give you a comparison. If you give the two datasets to Pointless, 
> >>> labelling them as different datasets, you can use Aimless to compare them
> >>> 
> >>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but 
> >>> still works and gives lots of statistics 
> >>> 
> >>> Phil
> >>> 
> >>> Sent from my iPhone
> >>> 
>  On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB 
>   wrote:
>  
>  I think that POINTLESS works with intensities rather than structure 
>  factors (I’m not sure if this can be changed). Also, SCALEIT gives a 
>  much more detailed breakdown (R factors as a function of resolution and 
>  differences in terms of sigmas etc) than POINTLESS WILL.
> >>

Re: [ccp4bb] Comparing two datasets

[Phil Evans]

If you want to merge them then you can use Pointless/Aimless/ctruncate, with 
the warning that the conversion from F to I is not ideal, and ctruncate should 
be set to regenerate F from I just as sqrt ie not apply the truncate procedure 
again. 
Pointless supersedes combat for this conversion 
Again, just for comparison use scaleit

Phil

Sent from my iPhone

> On 26 Jul 2022, at 13:33, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hello again, as far as I can tell, the question is about two already 
> merged/unique datasets which Mirek wishes to merge into one. As far as I can 
> tell/remember, Scaleit is for scaling datasets side-by-side to get 
> isomorphous differences, etc, and I don't know of a way that you could get it 
> to merge 2 datasets as Mirek requested. Probably I am wrong but Scaleit 
> R-factors are different from R-merge, although the latter might be a bit 
> dubious in the circumstances. Anyway, I think the Combat route is a viable 
> way of achieving what the questioner wants to achieve ;-0 
> 
> 
> Sent from ProtonMail mobile
> 
> 
> 
>  Original Message 
> On 26 Jul 2022, 12:25, John R Helliwell < jrhelliw...@gmail.com> wrote:
> 
> Dear Colleagues,
> Scaleit is a terrific program. 
> Amongst its strengths already listed I would also mention its breakdown table 
> with F so that in the strongest F reflections bin any systematic errors 
> between the two data sets can show up if the Rfactor is greater than about 
> 1%. 
> Greetings,
> John 
> Emeritus Professor John R Helliwell DSc
> 
> 
> 
> 
>> On 26 Jul 2022, at 11:40, Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> 
>> Not only does SCALEIT do the job - it presented useful plots and an 
>> informative log file..
>> Eleanor
>> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the 
>> columns from each Xtal will need different labels..)
>> 
>> On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:
>>> If you give Pointless Fs, it squares them to Is (not correct if the Fs have 
>>> been derived from the truncate procedure, but not too bad). It will then 
>>> give you a comparison. If you give the two datasets to Pointless, labelling 
>>> them as different datasets, you can use Aimless to compare them
>>> 
>>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but 
>>> still works and gives lots of statistics 
>>> 
>>> Phil
>>> 
>>> Sent from my iPhone
>>> 
 On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB 
  wrote:
 
 I think that POINTLESS works with intensities rather than structure 
 factors (I’m not sure if this can be changed). Also, SCALEIT gives a much 
 more detailed breakdown (R factors as a function of resolution and 
 differences in terms of sigmas etc) than POINTLESS WILL.
 
 Cheers,
 
 Andrew
 
> On 26 Jul 2022, at 09:24, LEGRAND Pierre 
>  wrote:
> 
> Hello Mirek,
> 
> A very quick approach for that is offered by pointless:
> 
> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
> or
> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
> 
> You will obtain a table looking like that, taking into account to 
> possible reindexing:
> 
> Alternative indexing scores relative to reference
>Alternative reindexingLklhd  CC R(E^2)Number 
> Cell_deviation
>  1  [h,k,l]  0.9930.9620.118 19150
>   0.08
>  2  [-k,h,l] 0.0070.0780.512 19150
>   0.87
> 
> 
> Best wishes,
> 
> Pierre Legrand
> PROXIMA-1 Beamline
> Synchrotron SOLEIL
> 
> De: "Nicolas Foos" 
> À: CCP4BB@JISCMAIL.AC.UK
> Envoyé: Mardi 26 Juillet 2022 08:36:35
> Objet: Re: [ccp4bb] Comparing two datasets
> 
> Hi Mirek, 
> 
> I am pretty sure XSCALE will do that for you : 
> https://xds.mr.mpg.de/html_doc/xscale_program.html
> 
> If not, maybe have a look on SHELXC in SIR mode. 
> 
> Hope this help. 
> 
> Nicolas
> 
> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
> Hi,
> I would like to calculate the R-merge for Fs from two datasets processed 
> from two different crystals. Tried to use Blend but got the message that 
> Blend requires R. Downloaded R but do not know how to tell CCP4 where it 
> is located on my Mac. Is there another program that would take two mtg 
> files and merge the Fs?
> Any help would be greatly appreciated. 
> 
> 
> Mirek
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
> --
> Nicolas Foos PhD - ARISE fellow
> https://orcid.org/-0003-2331-8399
> 
> EMBL Grenoble, McCarthy Team
> 71 av. des Martyrs,
>>

Re: [ccp4bb] Comparing two datasets

[Eleanor Dodson]

Indeed Jon you are right.
If you want to know whether to merge two dasta sets, use SCALEIT for
analysis..

If You actually want to merge the data. best to go back to each unmerged
and feed both into pointless/aimless etc, although you can cheat be letting
pointless square the given Fs then merge those two - not good practice but
possible..
Eleanor

On Tue, 26 Jul 2022 at 13:34, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello again, as far as I can tell, the question is about two already
> merged/unique datasets which Mirek wishes to merge into one. As far as I
> can tell/remember, Scaleit is for scaling datasets side-by-side to get
> isomorphous differences, etc, and I don't know of a way that you could get
> it to merge 2 datasets as Mirek requested. Probably I am wrong but Scaleit
> R-factors are different from R-merge, although the latter might be a bit
> dubious in the circumstances. Anyway, I think the Combat route is a viable
> way of achieving what the questioner wants to achieve ;-0
>
>
> Sent from ProtonMail mobile
>
>
>
>  Original Message 
> On 26 Jul 2022, 12:25, John R Helliwell < jrhelliw...@gmail.com> wrote:
>
>
> Dear Colleagues,
> Scaleit is a terrific program.
> Amongst its strengths already listed I would also mention its breakdown
> table with F so that in the strongest F reflections bin any systematic
> errors between the two data sets can show up if the Rfactor is greater than
> about 1%.
> Greetings,
> John
> Emeritus Professor John R Helliwell DSc
>
>
>
>
> On 26 Jul 2022, at 11:40, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> 
> Not only does SCALEIT do the job - it presented useful plots and an
> informative log file..
> Eleanor
> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously
> the columns from each Xtal will need different labels..)
>
> On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:
>
>> If you give Pointless Fs, it squares them to Is (not correct if the Fs
>> have been derived from the truncate procedure, but not too bad). It will
>> then give you a comparison. If you give the two datasets to Pointless,
>> labelling them as different datasets, you can use Aimless to compare them
>>
>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but
>> still works and gives lots of statistics
>>
>> Phil
>>
>> Sent from my iPhone
>>
>> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB <
>> and...@mrc-lmb.cam.ac.uk> wrote:
>>
>> I think that POINTLESS works with intensities rather than structure
>> factors (I’m not sure if this can be changed). Also, SCALEIT gives a much
>> more detailed breakdown (R factors as a function of resolution and
>> differences in terms of sigmas etc) than POINTLESS WILL.
>>
>> Cheers,
>>
>> Andrew
>>
>> On 26 Jul 2022, at 09:24, LEGRAND Pierre <
>> pierre.legr...@synchrotron-soleil.fr> wrote:
>>
>> Hello Mirek,
>>
>> A very quick approach for that is offered by pointless:
>>
>> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
>> or
>> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
>>
>> You will obtain a table looking like that, taking into account to
>> possible reindexing:
>>
>> Alternative indexing scores relative to reference
>>Alternative reindexingLklhd  CC R(E^2)Number
>> Cell_deviation
>>  1  [h,k,l]  0.9930.9620.118
>> 19150  0.08
>>  2  [-k,h,l] 0.0070.0780.512
>> 19150  0.87
>>
>>
>> Best wishes,
>>
>> Pierre Legrand
>> PROXIMA-1 Beamline
>> Synchrotron SOLEIL
>>
>> --
>> *De: *"Nicolas Foos" 
>> *À: *CCP4BB@JISCMAIL.AC.UK
>> *Envoyé: *Mardi 26 Juillet 2022 08:36:35
>> *Objet: *Re: [ccp4bb] Comparing two datasets
>>
>> Hi Mirek,
>>
>> I am pretty sure XSCALE will do that for you :
>> https://xds.mr.mpg.de/html_doc/xscale_program.html
>>
>> If not, maybe have a look on SHELXC in SIR mode.
>>
>> Hope this help.
>>
>> Nicolas
>> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
>>
>> Hi,
>> I would like to calculate the R-merge for Fs from two datasets processed
>> from two different crystals. Tried to use Blend but got the message that
>> Blend requires R. Downloaded R but do not know how to tell CCP4 where it is
>> located on my Mac. Is there another program that would take two mtg files
>> and merge the Fs?
>> Any help would be greatly appreciated.
>> Mirek
>>
>>
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>> --
>> Nicolas Foos PhD - ARISE fellowhttps://orcid.org/-0003-2331-8399
>>
>> EMBL Grenoble, McCarthy Team
>> 71 av. des Martyrs,
>> 38000 Grenoble FRANCE
>>
>> +33 4 57 42 84 67
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Comparing two datasets

[Jon Cooper]

Hello again, as far as I can tell, the question is about two already 
merged/unique datasets which Mirek wishes to merge into one. As far as I can 
tell/remember, Scaleit is for scaling datasets side-by-side to get isomorphous 
differences, etc, and I don't know of a way that you could get it to merge 2 
datasets as Mirek requested. Probably I am wrong but Scaleit R-factors are 
different from R-merge, although the latter might be a bit dubious in the 
circumstances. Anyway, I think the Combat route is a viable way of achieving 
what the questioner wants to achieve ;-0

Sent from ProtonMail mobile

 Original Message 
On 26 Jul 2022, 12:25, John R Helliwell wrote:

> Dear Colleagues,
> Scaleit is a terrific program.
> Amongst its strengths already listed I would also mention its breakdown table 
> with F so that in the strongest F reflections bin any systematic errors 
> between the two data sets can show up if the Rfactor is greater than about 1%.
> Greetings,
> John
>
> Emeritus Professor John R Helliwell DSc
>
>> On 26 Jul 2022, at 11:40, Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> 
>> Not only does SCALEIT do the job - it presented useful plots and an 
>> informative log file..
>> Eleanor
>> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the 
>> columns from each Xtal will need different labels..)
>>
>> On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:
>>
>>> If you give Pointless Fs, it squares them to Is (not correct if the Fs have 
>>> been derived from the truncate procedure, but not too bad). It will then 
>>> give you a comparison. If you give the two datasets to Pointless, labelling 
>>> them as different datasets, you can use Aimless to compare them
>>>
>>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but 
>>> still works and gives lots of statistics
>>>
>>> Phil
>>>
>>> Sent from my iPhone
>>>
 On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB 
  wrote:
>>>
 I think that POINTLESS works with intensities rather than structure 
 factors (I’m not sure if this can be changed). Also, SCALEIT gives a much 
 more detailed breakdown (R factors as a function of resolution and 
 differences in terms of sigmas etc) than POINTLESS WILL.

 Cheers,

 Andrew

> On 26 Jul 2022, at 09:24, LEGRAND Pierre 
>  wrote:
>
> Hello Mirek,
>
> A very quick approach for that is offered by pointless:
>
> pointless HKLREF 1_1_aimless.mtz HKLIN 2_1_aimless.mtz
> or
> pointless HKLREF 1_1_aimless.mtz XDSIN XDS_ASCII.HK
>
> You will obtain a table looking like that, taking into account to 
> possible reindexing:
>
> Alternative indexing scores relative to reference
> Alternative reindexing Lklhd CC R(E^2) Number Cell_deviation
> 1 [h,k,l] 0.993 0.962 0.118 19150 0.08
> 2 [-k,h,l] 0.007 0.078 0.512 19150 0.87
>
> Best wishes,
>
> Pierre Legrand
> PROXIMA-1 Beamline
> Synchrotron SOLEIL
>
> ---
>
> De: "Nicolas Foos" 
> À: CCP4BB@JISCMAIL.AC.UK
> Envoyé: Mardi 26 Juillet 2022 08:36:35
> Objet: Re: [ccp4bb] Comparing two datasets
>
> Hi Mirek,
>
> I am pretty sure XSCALE will do that for you : 
> https://xds.mr.mpg.de/html_doc/xscale_program.html
>
> If not, maybe have a look on SHELXC in SIR mode.
>
> Hope this help.
>
> Nicolas
>
> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
>
>> Hi,
>> I would like to calculate the R-merge for Fs from two datasets processed 
>> from two different crystals. Tried to use Blend but got the message that 
>> Blend requires R. Downloaded R but do not know how to tell CCP4 where it 
>> is located on my Mac. Is there another program that would take two mtg 
>> files and merge the Fs?
>> Any help would be greatly appreciated.
>>
>> Mirek
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> --
> Nicolas Foos PhD - ARISE fellow
> https://orcid.org/-0003-2331-8399
> EMBL Grenoble, McCarthy Team
> 71 av. des Martyrs,
> 38000 Grenoble FRANCE
>
> +33 4 57 42 84 67
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

 ---

>

Re: [ccp4bb] Comparing two datasets

[John R Helliwell]

Dear Colleagues,
Scaleit is a terrific program. 
Amongst its strengths already listed I would also mention its breakdown table 
with F so that in the strongest F reflections bin any systematic errors between 
the two data sets can show up if the Rfactor is greater than about 1%. 
Greetings,
John 
Emeritus Professor John R Helliwell DSc




> On 26 Jul 2022, at 11:40, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> 
> Not only does SCALEIT do the job - it presented useful plots and an 
> informative log file..
> Eleanor
> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the 
> columns from each Xtal will need different labels..)
> 
>> On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:
>> If you give Pointless Fs, it squares them to Is (not correct if the Fs have 
>> been derived from the truncate procedure, but not too bad). It will then 
>> give you a comparison. If you give the two datasets to Pointless, labelling 
>> them as different datasets, you can use Aimless to compare them
>> 
>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but 
>> still works and gives lots of statistics 
>> 
>> Phil
>> 
>> Sent from my iPhone
>> 
 On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB 
  wrote:
 
>>> I think that POINTLESS works with intensities rather than structure 
>>> factors (I’m not sure if this can be changed). Also, SCALEIT gives a much 
>>> more detailed breakdown (R factors as a function of resolution and 
>>> differences in terms of sigmas etc) than POINTLESS WILL.
>>> 
>>> Cheers,
>>> 
>>> Andrew
>>> 
 On 26 Jul 2022, at 09:24, LEGRAND Pierre 
  wrote:
 
 Hello Mirek,
 
 A very quick approach for that is offered by pointless:
 
 pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
 or
 pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
 
 You will obtain a table looking like that, taking into account to possible 
 reindexing:
 
 Alternative indexing scores relative to reference
Alternative reindexingLklhd  CC R(E^2)Number 
 Cell_deviation
  1  [h,k,l]  0.9930.9620.118 19150 
  0.08
  2  [-k,h,l] 0.0070.0780.512 19150 
  0.87
 
 
 Best wishes,
 
 Pierre Legrand
 PROXIMA-1 Beamline
 Synchrotron SOLEIL
 
 De: "Nicolas Foos" 
 À: CCP4BB@JISCMAIL.AC.UK
 Envoyé: Mardi 26 Juillet 2022 08:36:35
 Objet: Re: [ccp4bb] Comparing two datasets
 
 Hi Mirek, 
 
 I am pretty sure XSCALE will do that for you : 
 https://xds.mr.mpg.de/html_doc/xscale_program.html
 
 If not, maybe have a look on SHELXC in SIR mode. 
 
 Hope this help. 
 
 Nicolas
 
 On 25/07/2022 21:52, Cygler, Miroslaw wrote:
 Hi,
 I would like to calculate the R-merge for Fs from two datasets processed 
 from two different crystals. Tried to use Blend but got the message that 
 Blend requires R. Downloaded R but do not know how to tell CCP4 where it 
 is located on my Mac. Is there another program that would take two mtg 
 files and merge the Fs?
 Any help would be greatly appreciated. 
 
 
 Mirek
 
 
 
 
 
 To unsubscribe from the CCP4BB list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
 
 -- 
 Nicolas Foos PhD - ARISE fellow
 https://orcid.org/-0003-2331-8399

 EMBL Grenoble, McCarthy Team
 71 av. des Martyrs, 
 38000 Grenoble FRANCE

 +33 4 57 42 84 67
 
 To unsubscribe from the CCP4BB list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
 
 
 
 To unsubscribe from the CCP4BB list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
 
>>> 
>>> 
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Comparing two datasets

[Eleanor Dodson]

Not only does SCALEIT do the job - it presented useful plots and an
informative log file..
Eleanor
(You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the
columns from each Xtal will need different labels..)

On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:

> If you give Pointless Fs, it squares them to Is (not correct if the Fs
> have been derived from the truncate procedure, but not too bad). It will
> then give you a comparison. If you give the two datasets to Pointless,
> labelling them as different datasets, you can use Aimless to compare them
>
> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but
> still works and gives lots of statistics
>
> Phil
>
> Sent from my iPhone
>
> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB <
> and...@mrc-lmb.cam.ac.uk> wrote:
>
> I think that POINTLESS works with intensities rather than structure
> factors (I’m not sure if this can be changed). Also, SCALEIT gives a much
> more detailed breakdown (R factors as a function of resolution and
> differences in terms of sigmas etc) than POINTLESS WILL.
>
> Cheers,
>
> Andrew
>
> On 26 Jul 2022, at 09:24, LEGRAND Pierre <
> pierre.legr...@synchrotron-soleil.fr> wrote:
>
> Hello Mirek,
>
> A very quick approach for that is offered by pointless:
>
> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
> or
> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
>
> You will obtain a table looking like that, taking into account to possible
> reindexing:
>
> Alternative indexing scores relative to reference
>Alternative reindexingLklhd  CC R(E^2)Number
> Cell_deviation
>  1  [h,k,l]  0.9930.9620.118
> 19150  0.08
>  2  [-k,h,l] 0.0070.0780.512
> 19150  0.87
>
>
> Best wishes,
>
> Pierre Legrand
> PROXIMA-1 Beamline
> Synchrotron SOLEIL
>
> --
> *De: *"Nicolas Foos" 
> *À: *CCP4BB@JISCMAIL.AC.UK
> *Envoyé: *Mardi 26 Juillet 2022 08:36:35
> *Objet: *Re: [ccp4bb] Comparing two datasets
>
> Hi Mirek,
>
> I am pretty sure XSCALE will do that for you :
> https://xds.mr.mpg.de/html_doc/xscale_program.html
>
> If not, maybe have a look on SHELXC in SIR mode.
>
> Hope this help.
>
> Nicolas
> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
>
> Hi,
> I would like to calculate the R-merge for Fs from two datasets processed
> from two different crystals. Tried to use Blend but got the message that
> Blend requires R. Downloaded R but do not know how to tell CCP4 where it is
> located on my Mac. Is there another program that would take two mtg files
> and merge the Fs?
> Any help would be greatly appreciated.
> Mirek
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> --
> Nicolas Foos PhD - ARISE fellowhttps://orcid.org/-0003-2331-8399
>
> EMBL Grenoble, McCarthy Team
> 71 av. des Martyrs,
> 38000 Grenoble FRANCE
>
> +33 4 57 42 84 67
>
>
> --
>
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[ccp4bb] Improved EM validation with Q-score at the PDB

[David Armstrong]

Dear Colleagues,

Starting September 23, wwPDB validation of 3DEM structures for which 
there is both a model and an EM volume will include the Q-score metric 
(Pintilie, G., et al., 2020, Nat. Methods). This follows recommendations 
from the wwPDB/EMDB workshop on cryo-EM data management, deposition and 
validation in 2020 (white paper in preparation), as well as EM 
Validation Challenge events (Lawson C., et al., 2020, Struct. Dyn.; 
Lawson, et al., 2021, Nat. Methods). This will be the first quantitative 
parameter of residue and chain resolvability for EM maps in wwPDB 
validation reports and will provide an additional map-model assessment 
criterion.


The Q-score calculates the resolvability of atoms by measuring the 
similarity of the map values around each atom relative to a 
Gaussian-like function for a well-resolved atom. A Q-score of 1 
indicates that the similarity is perfect whilst closer to 0 indicates 
the similarity is low. If the atom is not well placed in the map then a 
negative Q-score value may be reported. Therefore, Q-score values in the 
reports will be in a range of -1 to +1.


The wwPDB EM validation reports will provide Q-scores for single 
particle, helical reconstruction, electron crystallography, and 
subtomogram averaging entries for which both an EM map and coordinate 
model have been deposited.


Validation reports (PDF files) will contain images of the average 
per-residue Q-scores colour-mapped onto ribbon models with views from 
three orthogonal directions. Similar images will also be introduced to 
visualize the per-residue atom-inclusion scores. A comparison of these 
two sets of images will assist in the visual assessment of the 
model-to-map fit and quality.


Please refer to the wwPDB news article for example images:
http://www.wwpdb.org/news/news?year=2022#62de9e5235ec5bb4ddb19a43

The validation reports will also contain a table of average per-chain 
values of both metrics (Q-score and atom inclusion) as well as their 
overall average values for the entire model.


The per-residue and the per-chain average atom-inclusion and Q-score 
values will also be provided in the mmCIF and XML formatted validation 
files. The mmCIF categories _pdbx_vrpt_summary_entity_fit_to_map and 
_pdbx_vrpt_model_instance_map_fitting will be introduced to include both 
the Q-scores and atom-inclusion values. The existing items, 
_pdbx_vrpt_summary_entity_geometry.average_residue_inclusion and 
_pdbx_vrpt_model_instance_geometry.residue_inclusion for atom inclusion 
will no longer be used.


The PDB Core Archive holds validation reports that assess each 3DEM 
model in the PDB along with the associated experimental 3D volume in 
EMDB. Validation reports of 3DEM structures (map and model) can be 
downloaded at the following wwPDB mirrors:


 * wwPDB: https://ftp.wwpdb.org/pub/pdb/validation_reports/
 * RCSB PDB: https://ftp.rcsb.org/pub/pdb/validation_reports/
 * PDBe: https://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/
 * PDBj: https://ftp.pdbj.org/pub/pdb/validation_reports/

The EMDB Core Archive holds validation reports that assess each EMDB 
map/tomogram entry. Validation reports for all EMDB volumes can be 
downloaded at the following wwPDB mirrors:


 * EMDB: https://ftp.ebi.ac.uk/pub/databases/emdb/validation_reports/
 * wwPDB: https://ftp.wwpdb.org/pub/emdb/validation_reports/
 * RCSB PDB: https://ftp.rcsb.org/pub/emdb/validation_reports/
 * PDBj: https://ftp.pdbj.org/pub/emdb/validation_reports/

Additional information about validation reports is available for EM 
map+model, EM map-only, and EM tomograms.


If you have any questions or queries about wwPDB validation, please 
contact us at validat...@mail.wwpdb.org.



Best regards,

James Tolchard

--
David Armstrong
Outreach and Training Lead
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544



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Re: [ccp4bb] Comparing two datasets

[Phil Evans]

If you give Pointless Fs, it squares them to Is (not correct if the Fs have 
been derived from the truncate procedure, but not too bad). It will then give 
you a comparison. If you give the two datasets to Pointless, labelling them as 
different datasets, you can use Aimless to compare them

But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but still 
works and gives lots of statistics 

Phil

Sent from my iPhone

> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB  
> wrote:
> 
> I think that POINTLESS works with intensities rather than structure factors 
> (I’m not sure if this can be changed). Also, SCALEIT gives a much more 
> detailed breakdown (R factors as a function of resolution and differences in 
> terms of sigmas etc) than POINTLESS WILL.
> 
> Cheers,
> 
> Andrew
> 
>> On 26 Jul 2022, at 09:24, LEGRAND Pierre 
>>  wrote:
>> 
>> Hello Mirek,
>> 
>> A very quick approach for that is offered by pointless:
>> 
>> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
>> or
>> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
>> 
>> You will obtain a table looking like that, taking into account to possible 
>> reindexing:
>> 
>> Alternative indexing scores relative to reference
>>Alternative reindexingLklhd  CC R(E^2)Number 
>> Cell_deviation
>>  1  [h,k,l]  0.9930.9620.118 19150  
>> 0.08
>>  2  [-k,h,l] 0.0070.0780.512 19150  
>> 0.87
>> 
>> 
>> Best wishes,
>> 
>> Pierre Legrand
>> PROXIMA-1 Beamline
>> Synchrotron SOLEIL
>> 
>> De: "Nicolas Foos" 
>> À: CCP4BB@JISCMAIL.AC.UK
>> Envoyé: Mardi 26 Juillet 2022 08:36:35
>> Objet: Re: [ccp4bb] Comparing two datasets
>> 
>> Hi Mirek, 
>> 
>> I am pretty sure XSCALE will do that for you : 
>> https://xds.mr.mpg.de/html_doc/xscale_program.html
>> 
>> If not, maybe have a look on SHELXC in SIR mode. 
>> 
>> Hope this help. 
>> 
>> Nicolas
>> 
>> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
>> Hi,
>> I would like to calculate the R-merge for Fs from two datasets processed 
>> from two different crystals. Tried to use Blend but got the message that 
>> Blend requires R. Downloaded R but do not know how to tell CCP4 where it is 
>> located on my Mac. Is there another program that would take two mtg files 
>> and merge the Fs?
>> Any help would be greatly appreciated. 
>> 
>> 
>> Mirek
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
>> -- 
>> Nicolas Foos PhD - ARISE fellow
>> https://orcid.org/-0003-2331-8399
>>
>> EMBL Grenoble, McCarthy Team
>> 71 av. des Martyrs, 
>> 38000 Grenoble FRANCE
>>
>> +33 4 57 42 84 67
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> 
> 
> 
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Re: [ccp4bb] Comparing two datasets

[Andrew Leslie - MRC LMB]

I think that POINTLESS works with intensities rather than structure factors 
(I’m not sure if this can be changed). Also, SCALEIT gives a much more detailed 
breakdown (R factors as a function of resolution and differences in terms of 
sigmas etc) than POINTLESS WILL.

Cheers,

Andrew

> On 26 Jul 2022, at 09:24, LEGRAND Pierre 
>  wrote:
> 
> Hello Mirek,
> 
> A very quick approach for that is offered by pointless:
> 
> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
> or
> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
> 
> You will obtain a table looking like that, taking into account to possible 
> reindexing:
> 
> Alternative indexing scores relative to reference
>Alternative reindexingLklhd  CC R(E^2)Number 
> Cell_deviation
>  1  [h,k,l]  0.9930.9620.118 19150  
> 0.08
>  2  [-k,h,l] 0.0070.0780.512 19150  
> 0.87
> 
> 
> Best wishes,
> 
> Pierre Legrand
> PROXIMA-1 Beamline
> Synchrotron SOLEIL
> 
> De: "Nicolas Foos" 
> À: CCP4BB@JISCMAIL.AC.UK
> Envoyé: Mardi 26 Juillet 2022 08:36:35
> Objet: Re: [ccp4bb] Comparing two datasets
> 
> Hi Mirek, 
> 
> I am pretty sure XSCALE will do that for you : 
> https://xds.mr.mpg.de/html_doc/xscale_program.html 
> 
> If not, maybe have a look on SHELXC in SIR mode. 
> 
> Hope this help. 
> 
> Nicolas
> 
> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
> Hi,
> I would like to calculate the R-merge for Fs from two datasets processed from 
> two different crystals. Tried to use Blend but got the message that Blend 
> requires R. Downloaded R but do not know how to tell CCP4 where it is located 
> on my Mac. Is there another program that would take two mtg files and merge 
> the Fs?
> Any help would be greatly appreciated. 
> 
> 
> Mirek
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 
> 
> -- 
> Nicolas Foos PhD - ARISE fellow
> https://orcid.org/-0003-2331-8399 
>
> EMBL Grenoble, McCarthy Team
> 71 av. des Martyrs, 
> 38000 Grenoble FRANCE
>
> +33 4 57 42 84 67
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 
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> 
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> 



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Re: [ccp4bb] Comparing two datasets

[LEGRAND Pierre]

Hello Mirek, 

A very quick approach for that is offered by pointless: 

pointless HKLREF 1_1_aimless.mtz HKLIN 2_1_aimless.mtz 
or 
pointless HKLREF 1_1_aimless.mtz XDSIN XDS_ASCII.HK 

You will obtain a table looking like that, taking into account to possible 
reindexing: 

Alternative indexing scores relative to reference 
Alternative reindexing Lklhd CC R(E^2) Number Cell_deviation 
1 [h,k,l] 0.993 0.962 0.118 19150 0.08 
2 [-k,h,l] 0.007 0.078 0.512 19150 0.87 


Best wishes, 

Pierre Legrand 
PROXIMA-1 Beamline 
Synchrotron SOLEIL 


De: "Nicolas Foos"  
À: CCP4BB@JISCMAIL.AC.UK 
Envoyé: Mardi 26 Juillet 2022 08:36:35 
Objet: Re: [ccp4bb] Comparing two datasets 



Hi Mirek, 


I am pretty sure XSCALE will do that for you : [ 
https://xds.mr.mpg.de/html_doc/xscale_program.html | 
https://xds.mr.mpg.de/html_doc/xscale_program.html ] 


If not, maybe have a look on SHELXC in SIR mode. 


Hope this help. 


Nicolas 
On 25/07/2022 21:52, Cygler, Miroslaw wrote: 


Hi, 
I would like to calculate the R-merge for Fs from two datasets processed from 
two different crystals. Tried to use Blend but got the message that Blend 
requires R. Downloaded R but do not know how to tell CCP4 where it is located 
on my Mac. Is there another program that would take two mtg files and merge the 
Fs? 
Any help would be greatly appreciated. 
Mirek 








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-- 
Nicolas Foos PhD - ARISE fellow [ https://orcid.org/-0003-2331-8399 | 
https://orcid.org/-0003-2331-8399 ] EMBL Grenoble, McCarthy Team
71 av. des Martyrs, 
38000 Grenoble FRANCE
   
+33 4 57 42 84 67 




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