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



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Re: [ccp4bb] Can anyone run refmac from the WINDOWS command prompt?

[Charles Ballard - UKRI STFC]

Hi Kevin

just checked and refmac runs happy for me from the CCP4Console.  Differences 
are that mine is in the default location, and that machine has not had an 
earlier version of ccp4 installed.

Can you check "set" to see what is set in the environment.

Charles

On 13 Feb 2019, at 11:29, Kevin Cowtan wrote:

Hi! Can anyone run refmac from the WINDOWS command prompt?

I've been experimenting with various combinations of environment variables, but 
I always get an error. The one instance of this error on google is an 
unanswered CCP4BB question.

Dictionary path has not been defined
Check the environment variable CLIBD_MON
Current value of CLIBD_MON is C:\Apps\CCP4-7\7.0\lib\data\monomers
It should be set to wherever_dict/dic/
===> Error: Wrong path for the dictionary files

 Refmac:  Wrong path for the dictionary files
 Refmac:  Wrong path for the dictionary files

The directory C:\Apps\CCP4-7\7.0\lib\data\monomers contains the following:

 Directory of C:\Apps\CCP4-7\7.0\lib\data\monomers

12/02/2019  15:42  .
12/02/2019  15:42  ..
12/02/2019  15:38  0
12/02/2019  15:39  1
12/02/2019  15:39  2
12/02/2019  15:39  3
12/02/2019  15:39  4
12/02/2019  15:39  5
12/02/2019  15:39  6
12/02/2019  15:39  7
12/02/2019  15:40  8
12/02/2019  15:40  9
12/02/2019  15:40  a
12/02/2019  15:40  b
12/02/2019  15:40  c
28/11/2016  21:43 7,640 COPYING
12/02/2019  15:40  d
28/11/2016  21:43 3,553 dnarna_basepairs.txt
28/11/2016  21:43 3,553 dnarna_basepairs_2.txt
28/11/2016  21:43 5,248 dnarna_params.txt
12/02/2019  15:40  e
27/04/2018  10:59   105,193 ener_lib.cif
28/11/2016  23:06   105,136 ener_one_lib.cif
12/02/2019  15:40  f
12/02/2019  15:40  g
12/02/2019  15:41  h
12/02/2019  15:41  i
12/02/2019  15:41  j
12/02/2019  15:41  k
12/02/2019  15:41  l
12/02/2019  15:41  list
12/02/2019  15:41  m
28/11/2016  21:43 1,372,146 mon_lib_ind.cif
28/11/2016  21:43 6,490,087 mon_lib_ind2.cif
28/11/2016  23:06   120 mon_lib_one_ind.cif
28/11/2016  23:06   396 mon_lib_one_ind2.cif
12/02/2019  15:41  n
31/08/2018  15:5235,312 new_entries.txt
31/08/2018  15:5223,685 not_replaced_entries.txt
12/02/2019  15:41  o
12/02/2019  15:41  p
28/11/2016  21:43 2,490,954 pdb_alt_names.txt
28/11/2016  21:43 7,794 pdb_v2to3.py
12/02/2019  15:41  q
12/02/2019  15:41  r
31/08/2018  15:5229,731 replaced_entries.txt
31/08/2018  15:52   754 revert_list.txt
12/02/2019  15:41  s
12/02/2019  15:42  t
28/11/2016  21:43   557 template_link.pdb
12/02/2019  15:42  u
12/02/2019  15:42  v
12/02/2019  15:42  w
31/08/2018  15:5224 windows_reserved_words.txt
12/02/2019  15:42  x
12/02/2019  15:42  y
12/02/2019  15:42  z
--
Professor Kevin Cowtan
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, York, YO10 5DD, UK
https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/

EMAIL DISCLAIMER: http://www.york.ac.uk/docs/disclaimer/email.htm



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[ccp4bb] shelxe update

[Charles Ballard - UKRI STFC]

Dear All

Ccp4 update 067 has been released and contains the updated shelxe

All the best

Charles



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[ccp4bb] CCP4 Study Weekend Early Bird ending

[Charles Ballard - UKRI STFC]

Dear All

a heads up that the early bird registration, and closing date for student 
bursaries, is Sunday 18th November 2018 i.e. this Sunday!

For more info see http://www.cvent.com/d/sgq8q6/1K?cpc=N7N8SK89V8N

Regards

Karen McIntyre
Scientific Computing Department - CCP4



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[ccp4bb] U-M Center for Structural Biology Research Fellow position

[Charles Ballard - UKRI STFC]

On behalf of Ashley Schork, University of Michigan:

Good morning,

I am reaching out on behalf of Jeanne Stuckey from the University of Michigan 
Life Sciences Institute Center for Structural Biology.

The Center for Structural 
Biology,
 (CSB) at the University of Michigan Life Sciences Institute seeks a 
post-doctoral candidate with crystallography experience, who is interested in 
developing cutting edge purification and crystallization technologies for RNA 
and RNA-Protein complexes. The CSB acts as the structural biology core for the 
Center for HIV RNA Studies (CRNA), which is a large consortium of researchers 
across the nation focusing on the structures, dynamics, interactions, and 
mechanisms of action of the HIV-1 RNA during the late phase of viral 
replication. Funding for these studies is provided by the National Institutes 
of General Medical Sciences, National Institutes of Health.  The post-doctoral 
fellow will work under the direction of Jeanne A. Stuckey, Ph.D, Managing 
Director of CSB and Research Associate Professor, and work in collaboration 
with members of the CSB.

Link to job posting: http://careers.umich.edu/job_detail/163107/research_fellow

The posting will be extended until October 18th. Would you be able to post to 
the CCP4 bulletin to reach those who would be interested in applying? Please 
let us know if you have any questions.

Ashley Schork
Structural Biology Program Coordinator
University of Michigan Life Sciences Institute
210 Washtenaw Ave
Ann Arbor, MI 48109-2216
734-647-8098 | ashls...@umich.edu

[U-M Life Sciences Institute logo]




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[ccp4bb] forming a 3D bioinformatics community

[Charles Ballard - UKRI STFC]

Structural bioinformatics is shaping its Community 

Relevance of structural informatics 
Structural bioinformatics has a broad impact across the life sciences and 
provides tools to archive, visualise, analyse, annotate, and predict the 
structure of biological macromolecules. Furthermore, the science of structural 
bioinformatics is traditionally very strong in Europe offering many software 
tools, methodologies, and databases, as well as community-wide prediction 
challenges. Its applications cover research activities from structural biology 
to drug discovery and personalized medicine. We envision that establishing an 
ELIXIR Community will facilitate deeper integration of our broad range of tools 
and services.
The leading research groups and activities in structural bioinformatics in 
Europe are already well represented within the ELIXIR nodes (e.g SWISS-MODEL). 
Several ELIXIR core data resources belong to this field, some of them, such as 
PDBe and CATH are of fundamental importance. Some of the highly cited ELIXIR 
tools also belong to the field of structural bioinformatics.  The 3D-BioInfo 
Community is building on this strength and links to several other 
infrastructures and EC projects. Tools and resources established by the 
3D-BioInfo Community have users in the field of structural biology (Instruct, 
iNEXT), cheminformatics (OpenScreen), system biology (ISBE), and molecular 
simulations (BioExcel) and these will benefit from collaborative projects with 
3D-BioInfo. The 3D-Bioinfo initiative will undoubtedly broaden this scope.

ELIXIR and instruct-ERIC 
The  instruct-ERIC is a most important collaborator and the 3D-BioInfo 
Community will coordinate closely with experimental structural biologists. We 
expect our collaborative projects to help link structural bioinformatic tools 
with emerging structural techniques, to help relate function to structure. This 
will attract new users and support the recognition of both ELIXIR and 
instruct-ERIC services. We expect potential collaborations to involve all five 
ELIXIR platforms (interoperability, data, tools, compute, training).

Goals of the community
The long term goals of the community include: improving integration of 
structural information with data on protein function, genomic variants, disease 
links, and drug action; developing platform for sharing, and benchmarking 
software for protein structure prediction, modeling protein assemblies and 
complexes with various ligands; integrating resources and tools for protein 
structural and evolutionary analyses; development and integration of various 
structural biology enabling tools, in close collaboration with Instruct-ERIC.

How to join 
If you are interested in participating, come to the launch meeting in Basel, 
October 19, 2018, to find out more. You will have the opportunity to present a 
poster and give a flash talk presenting your tools and suggesting how you might 
contribute to community activities. This meeting will be critical for 
collecting ideas for community activities, which will be the basis for a formal 
application to the ELIXIR Heads of Nodes to become an approved community in 
ELIXIR. 
If you would like to give a flash talk (one slide) to advertise a poster at the 
meeting on a proposed ELIXIR activity (involving collaborations across two or 
more groups within an ELIXIR node and preferably involving two or more nodes) 
please send a summary (maximum one page) to c.ore...@ucl.ac.uk outlining the 
groups and ELIXIR nodes involved and the ELIXIR platforms this activity would 
relate to i.e. interoperability, data, tools, compute or training. The proposed 
activity can involve multiple platforms.

Registration site: https://swissmodel.expasy.org/25years/

For information on the timelines for forming an ELIXIR Community in Structural 
Bioinformatics please see: 
https://drive.google.com/file/d/10a5PTWA8b00i7jYeuyOQQ0OXdn-EUoUI/view?usp=sharing
For information on suggested major themes and activities of the 3D-BioInfo 
Community – please see link below. You are welcome to add comments on 
additional activities.
https://drive.google.com/file/d/10DYf1uMg9jaHFOGX7gvKsHIAVRRwqyx1/view?usp=sharing




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[ccp4bb] ccp4 release 7.0 update 061 - major update to monomer library!

[Charles Ballard - UKRI STFC]

Dear All

ccp4 release update 061 is now available for updating and downloading.  It 
contains

 * monomer library
 - major update
 - 7000  new monomers
 - 8000 updated monomers

 * refmac
 - updated for new monomer library

 * buccaneer
 - new EM reference structure

This is a recommended update for all CCP4 users.

All the best

Charles (on behalf of the CCP4 core team)

ps - coming soon, ccp4i2 updates for molprobity, and dials 1.10




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[ccp4bb] ccp4 release 7.0 update 061

[Charles Ballard - UKRI STFC]

Dear All

ccp4 update 061 to release 7.0 is now available.  It contains

* DIALS 1.10.4 and XIA2 0.5.582
 - release notes: https://github.com/dials/dials/releases/tag/v1.10.0

* molprobity 4.4
 - scripts molprobity.molprobity, molprobity.clashscore, molprobity.cablam, 
probe, reduce, etc
 - http://molprobity.biochem.duke.edu/
 - thank you to Jane Richardson, Nigel Moriarty, Randy Read

* lorestr
 - update to use bundled molprobity.

This is available as an update to current installations, and as a direct 
download from the ccp4 site.

Coming soon:
 
 * major update to monomer library
 * molprobity integration to ccp4i2
 * DIALS gui update
 * additional reference structures for buccaneer.

All the best

Charles 


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[ccp4bb] SPring-8/CCP4 workshop on data collection and structure solution

[Charles Ballard - UKRI STFC]

Dear All

10 days to the registration closure for the second CCP4/Spring-8 (RIKEN) 
workshop running from 1-6 October 2018.

This workshop will cover data collection, processing and structure solution.  
Details are available at
http://www.ccp4.ac.uk/schools/Japan-2018 , with more to follow.  Registration 
is on the same site.  Registration will
close on 24 August.

Topics will include XDS (Kay Diederichs), DIALS (Graeme Winter), the CCP4 suite 
(myself and others),
PDB_REDO (Robbie Joosten), COOT and others. The format will cover data 
collection, lectures, tutorials and
problem solving, so students are encourages to bring their own data to work on.

Charles and Kunio.



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Re: [ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

[Charles Ballard - UKRI STFC]

[cid:a3a4faea-08e2-46af-88de-3bde456d9124@fed.cclrc.ac.uk]


Sorry for spamming you all on this, but these images keep on getting stripped 
for Armin and myself.

On 2 Aug 2018, at 16:51, Charles Ballard - UKRI STFC wrote:

> Begin forwarded message (on behalf of Armin Wagner)
> From: ahw78 mailto:armin.wag...@diamond.ac.uk>>
> Date: 2 August 2018 at 09:17:48 BST
> To: Eleanor Dodson 
> mailto:eleanor.dod...@york.ac.uk>>
> Cc: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>>
> Subject: Re: [ccp4bb] Sulphate or phosphate?
> Dear Eleanor,
>
> We can tune the wavelength over a large range (lambda = 1.2 – 6 A). This 
> allows collecting data above and below the absorption edges of Ca, K, Cl, S 
> and even P. Crystal, solvent and loop absorption are of course a problem for 
> the longest wavelengths, but so far we have done quite a fair amount of 
> studies around these absorption edges with strong signal above the edge and 
> obviously no signal below. Resolution in our setup is limited to around 3.2 A 
> at 5 A wavelength, but for anomalous difference fourier maps this is 
> sufficient. I have attached an example for a disulphide bridge which should 
> illustrate it better.
>
> Best regards,
>
>Armin
>
>
>
> [cid:image001.png@01D42A41.AE0B8B60]
>
> From: Eleanor Dodson 
> mailto:eleanor.dod...@york.ac.uk>>
> Date: Wednesday, 1 August 2018 at 19:09
> To: Armin Wagner 
> mailto:armin.wag...@diamond.ac.uk>>
> Cc: "ccp4bb@jiscmail.ac.uk<mailto:ccp4bb@jiscmail.ac.uk>" 
> mailto:ccp4bb@jiscmail.ac.uk>>
> Subject: Re: [ccp4bb] Sulphate or phosphate?
>
> I am not sure if you gave your wave length but it is always worth doing an 
> anomalous map, and looking at relativr peak heights for your known S 
> positions and the putative sulphate or phosphate.
> There are small differences in the expected f" at most wavelengths.
>
> Chemical arguments are doubtless better of Course!
> Eleanor
>
> On 1 August 2018 at 16:54, 
> armin.wag...@diamond.ac.uk<mailto:armin.wag...@diamond.ac.uk> 
> mailto:armin.wag...@diamond.ac.uk>> wrote:
> Dear David,
>
> The long-wavelength beamline I23 at Diamond 
> (http://www.diamond.ac.uk/Instruments/Mx/I23.html) can go all way down to the 
> phosphorous edge. While data quality will be obviously compromised by 
> absorption effects (we are working on this), for a reasonably well 
> diffracting crystal like yours we should be able to get anomalous difference 
> fourier maps from data collected above and below the sulphur edge (lambda ~5 
> A) to answer your question.
>
> We’ve published some test crystal work around the sulphur edge a while ago, 
> you might want to have a look here:
> https://doi.org/10.1016/j.nimb.2016.12.005
>
> The beamline is currently in an advanced commissioning phase accepting a 
> limited number of projects. So, please get into touch if you are interested. 
> We are currently sorting out a few more hardware and software aspects before 
> we can run the beamline as a standard user facility, but we have made a lot 
> of progress over the past months. There will be more details here on the 
> bulletin board ahead of the next call for proposals in autumn.
>
> Best regards,
>
>Armin
>
>
> Postdoc position for long-wavelength crystallography:
> https://vacancies.diamond.ac.uk/vacancy/post-doctoral-research-associate-355285.html
>
>
>
>
> On 31/07/2018, 14:38, "CCP4 bulletin board on behalf of David Schuller" 
> mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
> schul...@cornell.edu<mailto:schul...@cornell.edu>> wrote:
>
>How can one distinguish between a sulphate or phosphate in an electron
>density map? Both are present in the mother liquor, and resolution is in
>the range of 1.75 - 2.25 A
>
>
>--
>===
>All Things Serve the Beam
>===
>David J. Schuller
>modern man in a post-modern world
>MacCHESS, Cornell University
>
> schul...@cornell.edu<mailto:schul...@cornell.edu>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you

[ccp4bb] Fwd: [ccp4bb] Sulphate or phosphate? (Armin's figures)

[Charles Ballard - UKRI STFC]

Begin forwarded message:

[cid:image001.png@01D42A41.AE0B8B60]




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[ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

[Charles Ballard - UKRI STFC]

Begin forwarded message (on behalf of Armin Wagner)
From: ahw78 mailto:armin.wag...@diamond.ac.uk>>
Date: 2 August 2018 at 09:17:48 BST
To: Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>>
Cc: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>>
Subject: Re: [ccp4bb] Sulphate or phosphate?
Dear Eleanor,

We can tune the wavelength over a large range (lambda = 1.2 – 6 A). This allows 
collecting data above and below the absorption edges of Ca, K, Cl, S and even 
P. Crystal, solvent and loop absorption are of course a problem for the longest 
wavelengths, but so far we have done quite a fair amount of studies around 
these absorption edges with strong signal above the edge and obviously no 
signal below. Resolution in our setup is limited to around 3.2 A at 5 A 
wavelength, but for anomalous difference fourier maps this is sufficient. I 
have attached an example for a disulphide bridge which should illustrate it 
better.

Best regards,

Armin



[cid:image001.png@01D42A41.AE0B8B60]

From: Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>>
Date: Wednesday, 1 August 2018 at 19:09
To: Armin Wagner mailto:armin.wag...@diamond.ac.uk>>
Cc: "ccp4bb@jiscmail.ac.uk" 
mailto:ccp4bb@jiscmail.ac.uk>>
Subject: Re: [ccp4bb] Sulphate or phosphate?

I am not sure if you gave your wave length but it is always worth doing an 
anomalous map, and looking at relativr peak heights for your known S positions 
and the putative sulphate or phosphate.
There are small differences in the expected f" at most wavelengths.

Chemical arguments are doubtless better of Course!
Eleanor

On 1 August 2018 at 16:54, 
armin.wag...@diamond.ac.uk 
mailto:armin.wag...@diamond.ac.uk>> wrote:
Dear David,

The long-wavelength beamline I23 at Diamond 
(http://www.diamond.ac.uk/Instruments/Mx/I23.html) can go all way down to the 
phosphorous edge. While data quality will be obviously compromised by 
absorption effects (we are working on this), for a reasonably well diffracting 
crystal like yours we should be able to get anomalous difference fourier maps 
from data collected above and below the sulphur edge (lambda ~5 A) to answer 
your question.

We’ve published some test crystal work around the sulphur edge a while ago, you 
might want to have a look here:
https://doi.org/10.1016/j.nimb.2016.12.005

The beamline is currently in an advanced commissioning phase accepting a 
limited number of projects. So, please get into touch if you are interested. We 
are currently sorting out a few more hardware and software aspects before we 
can run the beamline as a standard user facility, but we have made a lot of 
progress over the past months. There will be more details here on the bulletin 
board ahead of the next call for proposals in autumn.

Best regards,

Armin


Postdoc position for long-wavelength crystallography:
https://vacancies.diamond.ac.uk/vacancy/post-doctoral-research-associate-355285.html




On 31/07/2018, 14:38, "CCP4 bulletin board on behalf of David Schuller" 
mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
schul...@cornell.edu> wrote:

How can one distinguish between a sulphate or phosphate in an electron
density map? Both are present in the mother liquor, and resolution is in
the range of 1.75 - 2.25 A


--
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University

schul...@cornell.edu



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[ccp4bb] CCP4 workshop at CSIR-IMTech, Chandigarh, 22-26 October 2018

[Charles Ballard - UKRI STFC]

Dear All

I am pleased to announce a CCP4 Crystallography School and Workshop at 
CSIR-IMTech, Chandigarh, India running from October 22 to October 26.

The course is intended mainly for graduate students and postdoctoral 
researchers in the area of structural biology. In some cases, assistant 
-professor-level applicants can be accepted as well. The school is not meant as 
an introductory level course to protein crystallography. It is designed more 
for applicants with reasonable expertise in crystallography and experience with 
the CCP4 suite. The purpose of the school is to address specific problems that 
the applicants face while processing diffraction data and while solving and 
refining novel structures. Applicants with already collected data will be given 
strong consideration, although this not a mandatory requirement.
Note: for the tuturials and practicals there is a limit of 35 students, 
lectures are open to all.


Application to the workshop is free of charge, but a letter from the supervisor 
or the professor will be required.Travel expenses will be the responsibility of 
the participant, accommodation and meals will be provided. There accommodation 
at the CSIR guest house.

Tutors will include:

Eleanor Dodson, Harry Powell, Udupi Ramagopal, members of the CCP4 team and 
ARP/wARP EMBL team.

Further details are available at

http://www.ccp4.ac.uk/schools/India-2018

All the best

Charles and Karthik




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Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Charles Ballard - UKRI STFC]

Update 055 should have reverted out ASP, and update 056 (coming real soon now) 
should fix the other issues.

Charles


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
"Weiergräber, Oliver H."
Sent: 26 April 2018 15:06
To: ccp4bb 
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Indeed, update 54 from Mar 29 seems to have messed up several monomer 
definitions and/or their handling in coot (the version distributed with ccp4):
- GLU and ASP contain lines referencing GLN and ASN, respectively, preventing 
coot from finding any chi angles.
- For GLN, chi angles appear twice in the coot torsion dialog.
- Many amino acid definitions now contain main chain torsion angles, which are 
erroneously listed as chi in coot.

The coot version available from Paul Emsleys website comes with its own version 
of the monomer library, which seems to work fine.

Best
Oliver


  PD Dr. Oliver H. Weiergräber
  Institute of Complex Systems
  ICS-6: Structural Biochemistry
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson 
[176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk]
Sent: Thursday, April 26, 2018 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Oops - oh dear - GLN labels should NOT appear in a list devoted to GLU!!


Well spotted..
Eleanor



On 26 April 2018 at 10:34, Chris Richardson 
mailto:chris.richard...@icr.ac.uk>> wrote:
Many thanks for explaining where it is going awry.

Looking at GLU.cif in the monomer library that is part of the CCP4 
distribution, it contains the following lines:

 GLN  chi1 N  CA CB CG   180.000   15.000   3
 GLN  chi2 CA CB CG CD   180.000   15.000   3
 GLN  chi3 CB CG CD OE10.000   30.000   2

In the monomer library you link, it has:

 GLU  chi1 N  CA CB CG   180.000   15.000   3
 GLU  chi2 CA CB CG CD   180.000   15.000   3
 GLU  chi3 CB CG CD OE20.000   30.000   2

Which makes more sense.

Thanks again,

Chris

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Huw Jenkins mailto:h.t.jenk...@me.com>>
Sent: 26 April 2018 09:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

> On 26 Apr 2018, at 09:19, Chris Richardson 
> mailto:chris.richard...@icr.ac.uk>> wrote:
>
> I've just compiled Coot on the same Mac using Fink, and the dialogue for this 
> version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the 
> same residue.

>From a quick look at the Fink coot.info it appears to get 
>the monomer library from here:

 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz

Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 
distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG  and CG <--> CD of Glu 14 
A from the RNase tutorial model.



Huw

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
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