Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

[Martyn Winn - STFC UKRI]

You can also try the CCPEM list for more cryoEM-orientated advice 
https://www.jiscmail.ac.uk/CCPEM and look in CCP-EM for more fitting, 
refinement, validation tools.

Certainly, the map doesn’t look 3A, unless you have filtered it for these 
pictures. The CC for the middle and C-terminal domains is not just low, but 
essentially zero. And as Basil points out, a map-model FSC of 22.3A at 0.5. So 
I think you need to look again at the initial fitting.

HTH
Martyn


From: CCP4 bulletin board  On Behalf Of Basil Greber
Sent: 10 January 2024 08:12
To: ccp4bb 
Subject: Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

Are you confident that your 3 Å resolution is correct? The map in the picture 
you supplied looks more like 5 Å, and the model vs. map FSC at 0.5 is 
apparently 20 Å (?).

Basil


Gesendet mit der mobilen Mail App

Am 10.01.24 um 05:57 schrieb Ketul Saharan
Von: "Ketul Saharan" 
Datum: 10. Januar 2024
An: CCP4BB@JISCMAIL.AC.UK
Cc:
Betreff: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.
Dear CCP4 community,
I am building a structure model from ~3.0 Å resolution cryo-EM map. The 
structure consists of seven chains, with each chain containing an N-, middle, 
and C-terminal domain. Although I attempted to directly fit the Alfa-fold 
model, it became evident that the protein exhibited some movement, leading to 
poor fitting of N-terminal. To improve the fitting, I segmented the alfa-fold 
model into two parts: i) the N-terminal and ii) the middle and C-terminal 
domain. These fragments were then fitted into the map. After a few rounds of 
refinement using coot and phenix, the model effectively fitted all seven chains.
The refinement resulted in a model to map correlation (CC mask) of over 60% for 
the N-terminus. However, even though the model appeared to fit well inside the 
map, particularly in the middle and C-terminus regions, the refining 
consistently resulted in a map to model correlation of 0%.
For your perusal, I have included the snapshot of the phenix refinement 
results, the correlation graph, and the fitted model within the map (displaying 
one chain out of seven).
I am not able to figure out why the correlation is so poor even after fine 
fitting of model to map.
Any support in resolving this issue would be much appreciated.

Thank,
Ketul Saharan


--
Ketul Saharan
Senior Research Fellow (Ph.D. Scholar)
Laboratory of Macromolecular Crystallography (Lab-8)
Institute of Life Sciences
Nalco Square, Chandrasekharpur
Bhubaneswar – 751023
Odisha State, INDIA

Phone: +91 8708290889
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correlation.tif[Image
 removed by sender.]
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model.tif[Image
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Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

[Martyn Winn - STFC UKRI]

You can also try the CCPEM list for more cryoEM-orientated advice 
https://www.jiscmail.ac.uk/CCPEM and look in CCP-EM for more fitting, 
refinement, validation tools.

Certainly, the map doesn’t look 3A, unless you have filtered it for these 
pictures. The CC for the middle and C-terminal domains is not just low, but 
essentially zero. And as Basil points out, a map-model FSC of 22.3A at 0.5. So 
I think you need to look again at the initial fitting.

HTH
Martyn


From: CCP4 bulletin board  On Behalf Of Basil Greber
Sent: 10 January 2024 08:12
To: ccp4bb 
Subject: Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

Are you confident that your 3 Å resolution is correct? The map in the picture 
you supplied looks more like 5 Å, and the model vs. map FSC at 0.5 is 
apparently 20 Å (?).

Basil


Gesendet mit der mobilen Mail App

Am 10.01.24 um 05:57 schrieb Ketul Saharan
Von: "Ketul Saharan" 
Datum: 10. Januar 2024
An: CCP4BB@JISCMAIL.AC.UK
Cc:
Betreff: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.
Dear CCP4 community,
I am building a structure model from ~3.0 Å resolution cryo-EM map. The 
structure consists of seven chains, with each chain containing an N-, middle, 
and C-terminal domain. Although I attempted to directly fit the Alfa-fold 
model, it became evident that the protein exhibited some movement, leading to 
poor fitting of N-terminal. To improve the fitting, I segmented the alfa-fold 
model into two parts: i) the N-terminal and ii) the middle and C-terminal 
domain. These fragments were then fitted into the map. After a few rounds of 
refinement using coot and phenix, the model effectively fitted all seven chains.
The refinement resulted in a model to map correlation (CC mask) of over 60% for 
the N-terminus. However, even though the model appeared to fit well inside the 
map, particularly in the middle and C-terminus regions, the refining 
consistently resulted in a map to model correlation of 0%.
For your perusal, I have included the snapshot of the phenix refinement 
results, the correlation graph, and the fitted model within the map (displaying 
one chain out of seven).
I am not able to figure out why the correlation is so poor even after fine 
fitting of model to map.
Any support in resolving this issue would be much appreciated.

Thank,
Ketul Saharan


--
Ketul Saharan
Senior Research Fellow (Ph.D. Scholar)
Laboratory of Macromolecular Crystallography (Lab-8)
Institute of Life Sciences
Nalco Square, Chandrasekharpur
Bhubaneswar – 751023
Odisha State, INDIA

Phone: +91 8708290889
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] 
124.png[Image
 removed by sender.]
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] 
correlation.tif[Image
 removed by sender.]
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] map to 
model.tif[Image
 removed by sender.]



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[ccp4bb] CoSeC Conference 2023 | Call for Presentations

[Martyn Winn - STFC UKRI]

Dear All,

Please see below an announcement from our umbrella organisation CoSeC. This is 
an annual meeting with a wider scope of computational science.

Cheers
Martyn


Computational Science Centre for Research Communities (CoSeC) 2023 Conference 
6th of December 2023
Call for Presentations - Deadline 31st October 2023
Further details -  call for presentations for speakers at the 2023 CoSeC 
Conference

The Computational Science Centre for Research Communities (CoSeC) invites 
submissions for its next annual conference, to be held at the Manchester Centre 
Convention Complex on Wednesday the 6th of December 2023 in conjunction with 
the Computing Insight UK event.

This is an opportunity for those involved in activities supported by CoSeC 
(Collaborative Computational Projects, High-End Consortia, and other activities 
within the UKRI Digital Research Infrastructure landscape) to present 
cross-cutting aspects of their work to like-minded researchers as well as 
leading members of the computing industry.

We invite abstract submissions around the following topics:


* Modelling, Simulation & Reconstruction: All aspects of computational 
science related to modelling, simulation and reconstruction. It is important 
that presented work be of interest to those outside of its immediate scientific 
community, with the most relevant work being that which has potential 
applications across the sciences.


* Scientific Reproducibility: Work relating to enabling reproducibility 
across computational science, from workflows through to ensuring data is 
produced and stored in accordance with the principles of FAIR (findable, 
accessible, interoperable, reproducible).


* Applied Artificial Intelligence and Machine Learning: The use or 
development of AI or ML data science approaches within the context of 
computational science. The most relevant work is likely to provide clear 
application beyond the fundamental and have potential applications across the 
sciences.


* Large Scale Computing for Computational Science: All aspects are 
invited for submission, from applied supercomputing (e.g. developments toward 
exascale and work related to the use of national infrastructure like ARCHER2) 
through to topics around accessibility, and usability of computational science 
methods or software on large scale computing platforms.

Accepted speakers will be able to present their work in Manchester with no 
associated registration fees as well as gain access to the full CIUK event on 
the 7th and 8th of December. Upon acceptance an optional extended version of 
the abstract will be published as part of the main CIUK conference proceedings.

For more details about CoSeC, the work we do and communities we support, please 
refer to our webpage: https://cosec.stfc.ac.uk/.

Contact CoSeC: co...@stfc.ac.uk



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[ccp4bb] FW: MRC Molecular and Cellular Medicine Board; Board Member Vacancy

[Martyn Winn - STFC UKRI]

Hi all. I'm forwarding this announcement on behalf of Robert Deller at the MRC:


As you may be aware, MRC conducts an annual recruitment exercise to fill 
vacancies across its boards and panels.

https://www.ukri.org/about-us/work-for-us/join-an-advisory-committee-panel-or-network/mrc-board-and-panel-vacancies/

The current recruitment exercise also includes a vacancy within the Molecular 
and Cellular Medicine Board focused on Structural Biology that I believe could 
appeal to individuals within the CCP4 community. The deadline for applications 
is the 30th September 2022.



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Re: [ccp4bb] help for motion correction

[Martyn Winn - STFC UKRI]

Might be better posted to cc...@jiscmail.ac.uk
m

-Original Message-
From: CCP4 bulletin board  On Behalf Of Jing
Sent: 16 July 2022 20:56
To: ccp4bb 
Subject: [ccp4bb] help for motion correction

Hello All,
 I have a question about gain reference file. When I try to work on Motion 
Correction on relion 3.1.3, it always reports an error message said "the size 
of image and the size of the gain reference do not match." Because of that 
error, I could not proceed motion correction of my data. The cryo EM facility 
gave me that refence file in dm4 format and I use dm2mrc to covert it to mrc 
file. May I ask which part that I did wrong? How to solve that error?
 Thank you



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Re: [ccp4bb] Help with One dimensional electron density calculation

[Martyn Winn - STFC UKRI]

Hi,

It’s not clear why you don’t use MAPMAN if that does what you want. If 
availability is the problem, it is still here 
https://github.com/martynwinn/Uppsala-Software-Factory

If you are prepared to do some Python, then 2 other options:

https://mrcfile.readthedocs.io/en/latest/readme.html  allows you to read in MRC 
file to a numpy array, and then you can you can average, interpolate, plot as 
you wish.  If your pore axis is aligned along Z and you want to average over 
the cross section, then this would be relatively straightforward.

https://gemmi.readthedocs.io/en/latest/grid.html  will also read in maps and 
manipulate.  It understands crystal symmetry, if that is what you have. It also 
has functions for interpolation.

HTH
Martyn

From: CCP4 bulletin board  On Behalf Of Ravikumar
Sent: 13 July 2022 19:18
To: ccp4bb 
Subject: [ccp4bb] Help with One dimensional electron density calculation


Dear all,

I would like to calculate One-dimension electron density profiles of the 
different number of ions bound to an ion channel. Are there any programs in 
CCP4/ Phenix which can do the same job as the MAPMAN (UPPSALA electron density 
server) program to extract the electron density values to plot electron density 
values versus pore axis? I have attached an example figure.

Thank you,
Ravikumar.



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[ccp4bb] abstract deadline for ECM33 now 31st May

[Martyn Winn - STFC UKRI]

Hi all,

A heads-up that the deadline for abstract submissions has been extended until 
the end of the month (31st May), see https://www.ecm33.fr/ and 
https://hopscotch.key4events.com/abstract.aspx?e=281

I'm chairing MS1 on "MX/Cryo-EM software development" and would very much like 
to have a good mix of talks (science domain, speaker, stage of development), so 
please consider putting an abstract in!

Hope to see you in Versailles,
Martyn




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this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
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[ccp4bb] MRC Biophysics and Biosimulation Community Engagement Event

[Martyn Winn - STFC UKRI]

[Posted on behalf of Robert Deller UKRI-MRC]

The MRC Data Science Strategic Advisory Group and BBSRC Transformative 
Technologies Strategy Advisory Panel have founded a task force to better 
understand the computing needs, including the associated training/skills, 
software and services, of the research communities that they support. The task 
force has designed an engagement exercise to support this aim, with the first 
planned meeting focusing on biomolecular and biophysical simulation on the 
afternoon of the 10th of June (13.00-16.00).

The workshop aims to
*   Better understand current usage of computing in research and future 
needs.
*   Explore the challenges, gaps and barriers to the use of computing, 
and the opportunities for the more effective use of existing capability.
*   Identify challenging research concepts/areas and the associated 
computing requirements and whether these could be enabled by access to larger 
scale computing capability.

If interested, please get in touch with 
ben.yarn...@mrc.ukri.org to learn more or 
register interest.

Secondly, we would also like to invite individuals to fill in this 
survey
 studying the practices and barriers that UK researchers from all disciplines 
face when using software and computing in their research. The results will 
contribute towards UKRI Digital Research Infrastructure policy and help direct 
funding, so it is vital that we hear from a broad range of researchers across 
the UKRI research community.



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should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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Re: [ccp4bb] Calculating RMSD of a loop

[Martyn Winn - UKRI STFC]

This is probably a good opportunity to say that the USF has moved to 
https://github.com/martynwinn/Uppsala-Software-Factory

Gerard asked for this so that they wouldn't be lost. I haven't put any effort 
into checking the binaries or compilation, but I will do what I can on a best 
effort basis ...

Others are welcome to contribute ...

cheers
m

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Degano 
Massimo
Sent: 17 September 2019 15:35
To: ccp4bb
Subject: Re: [ccp4bb] Calculating RMSD of a loop

Hi,

(good old) LSQMAN from the Uppsala Software Facotry will do this for you. First 
you align the structures based on the subset of atoms you want to match, then 
use the RMSD command to calculate the rmsd for the subset of atoms you are 
interested in.
Best wishes,

Massimo

--
Dr. Massimo Degano
Biocrystallography Unit
Dept. of Immunology, Transplantation, and Infectious Diseases
IRCCS Scientific Institute San Raffaele
via Olgettina 58
20132 Milan - Italy
email: degano.mass...@hsr.it
phone: +39-0226437152
fax: +39-0226434153
skype: maxdegano
ORCID: -0002-0787-1883
http://research.hsr.it/en/divisions/immunology-transplantation-and-infectious-diseases/biocrystallography.html


On 17 Sep 2019, at 15:31, Kyle Gregory 
<3632e92fcc15-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hi all,

What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha aligned 
structures?
Thought I could do this in Coot but I only see this if I align the specific 
loops, which I don't want to do.

Thanks,

Kyle


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[5xmille]

5xmille. INSIEME POSSIAMO continuare a scoprire nuove cure.

CODICE FISCALE 07636600962


Rispetta l'ambiente: non stampare questa mail se non è necessario.
Respect the environment: print this email only if necessary.



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Re: [ccp4bb] AW: [ccp4bb] how many crystallographers are there?

[Martyn Winn - UKRI STFC]

When I last looked a couple of years ago, the number of subscribers to the BB 
was 6396.  Given the many crystallographers who don’t subscribe to the BB, and 
the EMers who are not ex-crystallographers, I could well believe 20 or 30 
thousand.
HTH
m

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Manfred 
Weiss
Sent: 29 May 2019 21:16
To: ccp4bb
Subject: [ccp4bb] AW: [ccp4bb] how many crystallographers are there?

Roughly 3000 groups, i.e. 3 individuals, I would guess.
Hth,
Manfred

Von meinem Sony Xperia™-Smartphone gesendet

 Scott Horowitz schrieb 

Hi all, I was recently asked how many biological crystallographers plus cryo-EM 
users there are in the world (in relation to how many people could therefore be 
theoretically impacted by Foldit electron density tools, for the purposes of 
grant funding). I'm a bit at a loss as to even what order of magnitude to 
provide. Any thoughts about how to estimate a number?



Thanks,

Scott



Scott Horowitz, Ph.D.

Assistant Professor

Department of Chemistry & Biochemistry

Knoebel Institute for Healthy Aging

University of Denver



ECS Building

2155 E. Wesley Ave

Denver, CO 80208

Phone: 303-871-4326

Fax: 303-871-7915

Email: scott.horow...@du.edu

Office: Room 561   Lab: Room 505




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Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin



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[ccp4bb] CCPBioSim annual conference 2019, 4-6 Sept, Bristol

[Martyn Winn - UKRI STFC]

>From CCPBioSim. Note that the theme for the invited speakers is synthetic 
>biology and biomolecular design, but contributed talks and posters can be on 
>any aspect of biomolecular modelling and simulation.

m





Dear All,

We are pleased to announce that registration is now open for the 7th Annual 
CCPBioSim Conference - Frontiers in Biomolecular Simulation. Details and the 
link to the registration page can be found at 
http://www.ccpbiosim.ac.uk/ccpbiosim2019.

The 7th annual meeting of CCP-BioSim is organised jointly with the Molecular 
Graphics and Modelling Society and will have the theme of Modelling and 
Simulation for Synthetic Biology. The conference will showcase important 
advances in biomolecular modelling and simulation tools, technologies, 
interplay with experiment, and applications to biomolecular design and 
synthetic biology.

The conference will be taking place at the University of Bristol on 4-6 
September 2019, with the following invited speakers:
Prof. Charlotte Deane, University of Oxford, UK
Dr. Sarel Fleishman, Weizmann Institute of Science, Rehovot, Israel
Prof. Syma Khalid, University of Southampton, UK
Prof. Modesto Orozco, IRB Barcelona, Spain
Dr. Fabio Parmeggiani, University of Bristol, UK

Dr. Katarzyna Świderek, Universitat Jaume I, Valencia, Spain
Dr. Per-Olof Syrén, KTH Royal Institute of Technology, Stockholm, Sweden

Submissions for contributed posters and talks are highly encouraged. Whilst the 
conference specifically highlights the use of modelling and simulation for 
biomolecular design and synthetic biology, presentations across the broad area 
of biomolecular simulation and modelling are very welcome.

On behalf of the organizing committee,

Marc van der Kamp (University of Bristol, co-chair)
Adrian Mulholland (University of Bristol, co-chair)
Sarah Harris (University of Leeds)
Ross Anderson (University of Bristol)
Sarah Fegan (STFC, Daresbury)




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Re: [ccp4bb] Current "best" software for computing volumes of active sites

[Martyn Winn - UKRI STFC]

Hi,

At the request of Gerard, I have rescued the USF packages into github 
https://github.com/martynwinn/Uppsala-Software-Factory

So far, I have done nothing with this, so no guarantees that the code still 
compiles or that the old binaries still work.

Nevertheless, it does contain a cavity.lib file for voidoo (in fact, 4 
variants). Perhaps that helps.

cheers
Martyn

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Fred 
Vellieux
Sent: 04 April 2019 07:24
To: ccp4bb
Subject: [ccp4bb] Current "best" software for computing volumes of active sites

Hi CCP4BBers,

With software constantly changing, new versions arriving to us and new 
software reaching the intended audience, I am looking for the most 
appropriate piece(s) of software to compute the volume of active site 
"cavities" in related 3D structures.

I have tried to use Voidoo however I do not know where to download an 
initial (and fairly comprehensive) cavity.lib file which I'd modify if 
need be. The links on the USF web site appear to be broken.

I am running Linux.

Thanks for the advice,

Fred. Vellieux



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Re: [ccp4bb] CTF correction of tomograms

[Martyn Winn - UKRI STFC]

There is an IMOD mailing list, and David Mastronarde is very good at answering 
queries. See https://bio3d.colorado.edu/imod/joinlist.html

There seems to be a tutorial for ctfplotter at 
https://bio3d.colorado.edu/imod/doc/CTFexamples.html and the manual 
https://bio3d.colorado.edu/imod/doc/man/ctfplotter.html has some explanation of 
noise files.

You might also want to look into NovaCTF 
https://www.ncbi.nlm.nih.gov/pubmed/28743638 which should be compatible with 
reconstruction in IMOD.

Finally, although the IMOD list is the most appropriate, you could also try the 
CCP-EM list https://www.jiscmail.ac.uk/CCPEM

HTH
m

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carlos 
Lopez
Sent: 09 January 2019 15:54
To: ccp4bb
Subject: [ccp4bb] CTF correction of tomograms

Hi,

I am not sure how to correct CTF in tomography data. I am trying to excute 
ctfplotter, from IMOD, but it cannot read the Noise files. Could someone 
provide a small explanation, or a clear alternative? I have been looking for 
tutorials, but I cannot find nothing clear for tomography.

Many thanks




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Re: [ccp4bb] fit pdb on cryo-EM map

[Martyn Winn - UKRI STFC]

Use CCP-EM!  Which has your favourite CCP4 programs adapted for cryoEM, plus 
some others. See www.ccpem.ac.uk

There is a hierarchy from rigid body fitting (of your xtal monomer), to 
flexible fitting (to account for adjustments in the new form), to de novo 
building and refinement. What you can do will depend on the EM resolution 
(local as well as global).

Look out for our annual Icknield workshops that provide training on model 
fitting and building.

HTH
Martyn

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Monika 
Pathak
Sent: 04 December 2018 11:04
To: ccp4bb
Subject: [ccp4bb] fit pdb on cryo-EM map

Hi there

Please can I get some suggestion on how to build a pdb into a cryoEM map.
To be more clear I have a crystal structure solved as dimer in asymmetric unit 
and I am trying to model it as a trimer form (biologically relevant) using 
cryo-EM map of a very similar homologue protein as a template.
I thank in advance for your help.
Thanks
Regards

Monika
School of Life Sciences
University of Nottingham
UK









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Re: [ccp4bb] building into EM map

[Martyn Winn]

You could look at the CCP-EM software http://www.ccpem.ac.uk/download.php which 
includes CCP4 programs adapted to cryoEM (e.g. allowing input of cryoEM map).

There is a range of possibilities from rigid body fitting of components, 
flexible fitting or de novo building.  At 4 A, you may struggle with de novo 
building, though of course you may have regions where the local resolution is 
better.

There are some tutorials etc here 
http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

Good luck
Martyn

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Natalia O
Sent: 23 January 2018 20:04
To: ccp4bb
Subject: [ccp4bb] building into EM map

Hello,

I am new to building into an EM map, and I wonder if I could get a 
recommendation for some standard routine for programs to use. I tried "find 
helixes and strands" tool in phenix, it found some secondary structure 
elements, however, it seems that there is more that could be done 
automatically. Is there any standard set of tools to use for automatic building 
in EM map of about 4A resolution?

Thank you!

-Natalia

[ccp4bb] FW: CCPBioSim conference

[Martyn Winn]

on behalf of Jon Essex:


===

The 5th annual CCPBioSim conference "Frontiers of Biomolecular

Simulation" will be held at the University of Southampton, from

Wednesday 13th to Friday 15th September 2017. The aim of the event is to

bring together computational and experimental scientists with an

interest in developing and applying biomolecular simulation techniques

to their work.



The deadline for submission of abstracts for a contributed oral or

poster presentation is July 21st and the deadline for early-bird

registration fees is June 1st.



Further information regarding registration, schedule, abstract

submission, and other matters is available at:



http://www.ccpbiosim.ac.uk/ccpbiosim2017



Confirmed Invited Speakers:



 D.r Lucy Forrest, NIH/NINDS, MD, USA

 Prof. Franca Fraternali, King's College London, London, UK.

 Prof. Francesco Gervasio, University College London, London, UK

 Dr. Bettina Keller, Freie Universität Berlin, Berlin, Germany

 Prof. Alex MacKerell, University of Maryland, Baltimore, MD, USA

 Dr. Sylvia McLain, University of Oxford, Oxford, UK

 Prof. Vicent Moliner, University Jaume I, Castellon, Spain

 Prof. Michele Vendruscolo, University of Cambridge, Cambridge, UK



Best wishes from the organising committee,



Dr David Huggins

University of Cambridge, UK



Professor Jonathan Essex

University of Southampton, UK



Dr Edina Rosta

King's College London, UK



Dr Marc van der Kamp

University of Bristol, UK

===






Professor Jonathan W. Essex
Chairman, Institute for Complex Systems Simulation (ICSS)
Co-Director, EPSRC Centre for Doctoral Training in Theory and Modelling in 
Chemical Sciences
School of Chemistry
University of Southampton
Highfield
Southampton
SO17 1BJ
United Kingdom
Phone: +44 (0)23 8059 2794
Fax: +44 (0)23 8059 3781
Mobile: +44 (0)7850 928919
Email: j.w.es...@soton.ac.uk
http://www.soton.ac.uk/~chemphys/jessex
http://www.tmcs.ac.uk
http://www.icss.soton.ac.uk/

Re: [ccp4bb] Cryo-em model building with Balbes

[Martyn Winn]

Hi,

MRC is a map format, and doesn't hold the reciprocal space structure factors 
that Balbes expects, and that are referred to in the error message. Yes, you 
will need to calculate structure factors, which are held in the MTZ format. 

Simplest way is to use Refmac, which deals with issues like box size and map 
sharpening. See step 1) described at   
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html#id.seab0879x62k
 

More options for model fitting, building and refinement are on the CCP-EM page 
for the recent Icknield workshop:  
http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

HTH
m

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of cheng tat 
cheung
Sent: 25 April 2017 16:18
To: ccp4bb
Subject: Re: [ccp4bb] Cryo-em model building with Balbes

phenix.map_to_structure_factors can do the conversion, and then all the 
crystallographic tools for model building should be ready to use.

Tat

Sent from my iPhone

> On 25 Apr 2017, at 10:36 AM, KL Ho 
> <05c3a58110fa-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Dear All,
> 
> We are interested to build an atomic model on a 3.7 A cryo-em map with 
> BALBES-MOLREP pipeline. The map is currently in mrc format. It cannot be read 
> by BALBES (the error message is structure factor file size exceed limit). I 
> was wondering should I convert the mrc file to mtz format? Any idea how to 
> convert the mrc to mtz? 
> 
> Many thanks in advance. 
> 
> Best wishes
> Kok-Lian

[ccp4bb] EMBO practical course on image processing for cryo-electron microscopy

[Martyn Winn]

Posted on behalf  of Elena Orlova...

Dear All,
It is a pleasure to announce that we are running the next EMBO practical course 
on image processing for cryo-electron microscopy in Birkbeck College , ISMB, 
London . This 10 day course will be held in  September (5 - 15),  2017. 
You can find our announcement on the following sites:
Twitter ( https://twitter.com/EMBOevents/status/818487485814730759 ), 
Facebook ( https://www.facebook.com/events/590421591166869/ ) 
EMBO events calendar ( http://www.embo.org/events/events-calendar ).
Birkbeck College 
(http://www.bbk.ac.uk/biology/about-us/events/image-processing-for-cryo-electron-microscopy-1)

Deadline for applications: Monday 15 May 2017 
The aim of the course is to teach the basic principles and practical aspects of 
image processing to bioscientists and structural biologists wishing to 
determine macromolecular structures by cryo electron microscopy (EM). The 
course will concentrate on processing of single particle images, and will be 
aimed at advanced PhD students and postdocs working on projects producing cryo 
EM images for structural analysis. Familiarity with UNIX would be an advantage. 
The first half of the day will include two 50-minutes lectures and discussions. 
A 3-hour practical would take place in the afternoon, with discussion time at 
the end. After dinner there will be invited speaker lectures or student 
presentations.

Applications are invited from PhD students and researchers in EM. Please apply 
now via http://meetings.embo.org/event/17-cryo-em  the page  is on EMBO site. 
On this pages you will find   leading  scientists in the field who will give 
insightful  lectures.
A time table is a preliminary one and can be amended.
Applications are invited from PhD students and researchers in EM. 
Applications should include: 
a Curriculum vitae; a publication list; a short description of your current 
work and future plans; an explanation of why attendance at the course would 
further the applicant's own research; and a letter of recommendation from the 
applicant's supervisor.

Sincerely yours
Elena Orlova, Helen Saibil, Peter Rosenthal, and Carolyn Moores

*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*

Re: [ccp4bb] Docking crystal structure into EM model

[Martyn Winn]

Yes, it can certainly be error-prone and subjective. A nice survey of issues 
and scoring functions (including use of Laplacian filter) is in 
http://www.ncbi.nlm.nih.gov/pubmed/21296161

You might find some useful tips in our recent workshops:

http://www.ccpem.ac.uk/training/icknield_2016/icknield_2016.php
http://i2pc.cnb.csic.es/hands-on-course-may-2016.html

In practice, most EMers use Chimera with manual placement followed by local 
optimisation. Still plenty of scope of over-imaginative fitting...

HTH
m

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Filip Van 
Petegem
Sent: 08 August 2016 20:09
To: ccp4bb
Subject: Re: [ccp4bb] Docking crystal structure into EM model

Hi Zbyszek,

I'm referring to the fitting contrast increase in the Situs methods slide:
http://situs.biomachina.org/fft.pdf

Perhaps this is what you meant anyway, but there's no explicit mention of 
"image sharpening".  The main advantage, as I understand it, is to increase 
fitting contrast by making the inside density negative, and the contour 
positive.  This allows both contour and volume matches to contribute to the 
correlation coefficient.  From experience using this on many occasions, the 
results are far superior compared to using standard cross-correlation 
coefficients (important, this is with cryo-EM maps at resolutions worse than 
10A). Where standard correlation coefficients failed miserably, the filtered 
method allowed the correct location an orientation to be found, as later 
verified experimentally.


Filip Van Petegem



On Mon, Aug 8, 2016 at 11:41 AM, 
mailto:zbys...@work.swmed.edu>> wrote:
Laplacian filter is a particular form of image sharpening, being a
high-pass filer with coefficient increasing quadratically with resolution.
If it produces more interpretable map image, the map density definitely
needs some form of sharpening.

For experimental images of atomic structures, there is no theoretical
justification why Laplacian filter should be better than Gaussian
sharpening, with adjustable B-factor, as present in Coot, for example.

Zbyszek Otwinowski

> Hi Sam,
>
> I highly recommend the 'colores' routine in Situs (
> http://situs.biomachina.org/).  It has the advantage of being able to
> apply
> a Laplacian filter to enhance surface matching. This feature is quite
> crucial when the resolution of the map is not very high, and when the
> crystal structure only represents a small fraction of the entire
> structure.
>
> Best regards,
>
> Filip Van Petegem
>
>
>
> On Mon, Aug 8, 2016 at 10:00 AM, Sam Tang 
> mailto:samtys0...@gmail.com>> wrote:
>
>> Dear all
>>
>> Sorry for this thread which is slightly off-topic.
>>
>> We have recently got a crystal structure of a protein which forms part
>> of
>> a higher order complex, the cryo-EM model of which has been solved and
>> published. In order to visualize some structural features we try to
>> place
>> this protein into the EM map of the complex in Pymol manually. However
>> limitation in resolution of the EM map renders this process error-prone
>> and
>> indeed subjective.
>>
>> I wonder if anyone has similar experience and could advise a better
>> strategy in doing so.
>>
>> Thanks in advance.
>>
>> Sam
>>
>> Biochemistry Programme, School of Life Sciences, CUHK
>>
>>
>
>
> --
> Filip Van Petegem, PhD
> Associate Professor
> The University of British Columbia
> Dept. of Biochemistry and Molecular Biology
> 2350 Health Sciences Mall - Rm 2.356
> Vancouver, V6T 1Z3
>
> phone: +1 604 827 4267
> email: filip.vanpete...@gmail.com
> http://crg.ubc.ca/VanPetegem/
>

Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353



--
Filip Van Petegem, PhD
Associate Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3

phone: +1 604 827 4267
email: filip.vanpete...@gmail.com
http://crg.ubc.ca/VanPetegem/

[ccp4bb] CCPBioSim one day training workshop on free energy calculations

[Martyn Winn]

Dear all,

CCPBioSim are running a free one-day training course on performing free energy 
calculations in protein systems. The particular focus will be on estimating 
protein-ligand binding affinities, but the role of solvation in mediating 
protein-ligand interactions will also be explored.

Date: Tuesday 25th November, 2014
Location: University of Southampton, Highfield Campus, Building 36, Room 2065
Instructors: Dr Julien Michel (Edinburgh), Dr Sam Genheden (Southampton), Dr 
Richard Bradshaw (Southampton), Dr Greg Ross (Southampton), Ana Cabedo Martinez 
(Southampton)

Further details are available at 
http://www.ccpbiosim.ac.uk/workshops/2ndFreeEnergy and registration is open at 
https://eventbooking.stfc.ac.uk/news-events/ccpbiosim-free-energy-methods-for-modelling-of-protein-ligand-interactions-250
 

Cheers
Martyn

on behalf of Professor Jonathan W. Essex (Southampton)

*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*


--
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Re: [ccp4bb] CCPBioSim 1-day training course: How to set up a protein simulation, 29th Sept, Oxford

[Martyn Winn]

A reminder of this free 1-day training course.

The deadline for expressing interest is 14th September (this Sunday).

Cheers
Martyn

-Original Message-
From: Winn, Martyn (STFC,DL,SC) 
Sent: 06 August 2014 22:25
To: 'ccp4bb@jiscmail.ac.uk'
Subject: CCPBioSim 1-day training course: How to set up a protein simulation, 
29th Sept, Oxford

Dear All,

CCPBioSim are running a free 1-day training course aimed at beginners wishing 
to learn the practicalities of setting up a protein molecular dynamics 
simulation.

Date: Monday, 29th September 2014
Location: Donald Broadbent Lab, Department of Experimental Psychology, 
Tinbergen Building, 9 South Parks Road, Oxford, OX1 3UD
Instructors: Syma Khalid (Southampton) and Phill Stansfeld (Oxford)

Further details are available at 
http://www.ccpbiosim.ac.uk/workshops/3rdSetupSimulation and registration is 
open at 
https://eventbooking.stfc.ac.uk/news-events/ccpbiosim-how-to-set-up-a-protein-simulation-228

Cheers
Martyn

*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*

--
Scanned by iCritical.

[ccp4bb] Time on the UK national supercomputing service (Archer) from the HECBioSim consortium

[Martyn Winn]

Dear All,

The UK-funded Consortium for High End Computing in biomolecular simulation 
(HECBioSim) has time on the national supercomputing service (Archer) to 
allocate to biomolecular simulation projects. The next deadline for 
applications is on 15th of September.

Applicants should be aware that this 4th panel has a higher number of resources 
to allocate, therefore we are in a position to award slightly larger projects 
(~30-40kAUs) alongside more standard applications. Note that the PI on the 
proposal must be UK-based. Please see our website for details on how to apply: 

http://www.hecbiosim.ac.uk/index.php/applications

We look forward to hearing from you.

Martyn
(on behalf of HECBioSim consortium)

PS Bearing in mind the crystallographic audience, if anyone has computational 
projects that they think would benefit from Archer, but you don't know if they 
are suitable for HECBioSim, please drop me a line.

*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*


--
Scanned by iCritical.

[ccp4bb] CCPBioSim 1-day training course: How to set up a protein simulation, 29th Sept, Oxford

[Martyn Winn]

Dear All,

CCPBioSim are running a free 1-day training course aimed at beginners wishing 
to learn the practicalities of setting up a protein molecular dynamics 
simulation.

Date: Monday, 29th September 2014
Location: Donald Broadbent Lab, Department of Experimental Psychology, 
Tinbergen Building, 9 South Parks Road, Oxford, OX1 3UD
Instructors: Syma Khalid (Southampton) and Phill Stansfeld (Oxford)

Further details are available at 
http://www.ccpbiosim.ac.uk/workshops/3rdSetupSimulation and registration is 
open at 
https://eventbooking.stfc.ac.uk/news-events/ccpbiosim-how-to-set-up-a-protein-simulation-228

Cheers
Martyn

*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*

--
Scanned by iCritical.

[ccp4bb] *abstract deadline 10th March* 3rd annual CCP-BioSim conference - Frontiers of Biomolecular Simulation - University of Edinburgh - 21st-23rd May 2014

[Martyn Winn]

Quick reminder that the deadline for abstracts for the CCPBioSim annual 
conference is next Monday.

Cheers
Martyn


Dear Colleagues,

The third annual CCP-BioSim conference will be held at the John McIntyre 
conference centre, Edinburgh First, from Wednesday 21st to Friday 23rd May 
2014. The aim of the event is to bring together computational and experimental 
scientists with an interest in developing and applying biomolecular simulation 
techniques to their work.

The deadline for submission of abstracts for a contributed oral or poster 
presentation is March the 10th.

Further information regarding registration, schedule, abstract submission and 
other matters is available at:
http://www.ccpbiosim.ac.uk/?q=annualconfs/conf2014

Confirmed Invited Speakers

* Alexandre Bonvin, Bijvoet Center for Biomolecular Research, Utrecht, 
Netherlands
* Cecilia Clementi, Rice University, Department of Chemistry, USA
* Michael Gilson, Skaggs School of Pharmacy and Pharmaceutical Sciences, 
University of California San Diego, USA
* Bert de Groot, Max Planck Institute for Biophysical Chemistry, Göttingen, 
Germany
* Frauke Gräter, Heidelberg Institute of Theoretical Studies, Germany
* Gerhard Hummer, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
* Michael Mazanetz, Evotec UK Ltd. , UK
* Irina Tikhonova, School of Pharmacy, Queen's University Belfast, UK

--
Dr. Julien Michel,
Royal Society University Research Fellow
Room 263
School of Chemistry
University of Edinburgh
West Mains Road
Edinburgh, EH9 3JJ
United Kingdom
phone:   +44 (0)131 650 4797
http://www.julienmichel.net/
-

-- 
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[ccp4bb] *conference reminder* 3rd annual CCP-BioSim conference - Frontiers of Biomolecular Simulation - University of Edinburgh - 21st-23rd May 2014

[Martyn Winn]

As advertised at the Study Weekend, CCPBioSim is the sister CCP in biomolecular 
simulation. The annual conference will take place in Edinburgh in May, see 
details below.

Cheers
Martyn


Dear Colleagues,

The third annual CCP-BioSim conference will be held at the John McIntyre 
conference centre, Edinburgh First, from Wednesday 21st to Friday 23rd May 
2014. The aim of the event is to bring together computational and experimental 
scientists with an interest in developing and applying biomolecular simulation 
techniques to their work.

The deadline for submission of abstracts for a contributed oral or poster 
presentation is March the 10th.

Further information regarding registration, schedule, abstract submission and 
other matters is available at:
http://www.ccpbiosim.ac.uk/?q=annualconfs/conf2014

Confirmed Invited Speakers

* Alexandre Bonvin, Bijvoet Center for Biomolecular Research, Utrecht, 
Netherlands
* Cecilia Clementi, Rice University, Department of Chemistry, USA
* Michael Gilson, Skaggs School of Pharmacy and Pharmaceutical Sciences, 
University of California San Diego, USA
* Bert de Groot, Max Planck Institute for Biophysical Chemistry, Göttingen, 
Germany
* Frauke Gräter, Heidelberg Institute of Theoretical Studies, Germany
* Gerhard Hummer, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
* Michael Mazanetz, Evotec UK Ltd. , UK
* Irina Tikhonova, School of Pharmacy, Queen's University Belfast, UK

--
Dr. Julien Michel,
Royal Society University Research Fellow
Room 263
School of Chemistry
University of Edinburgh
West Mains Road
Edinburgh, EH9 3JJ
United Kingdom
phone:   +44 (0)131 650 4797
http://www.julienmichel.net/
-

-- 
Scanned by iCritical.

Re: [ccp4bb] ccp4 man-pages

[Martyn Winn]

Yes, that's more or less what we do/did. It was in a makefile somewhere.

Cheers
Martyn

> -Original Message-
> From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de]
> Sent: 15 November 2013 15:00
> To: Winn, Martyn (STFC,DL,SC)
> Cc: ccp4bb
> Subject: Re: [ccp4bb] ccp4 man-pages
> 
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Dear Martyn,
> 
> thanks for the hint about lynx. I could create the 'man'-pages with #>
> cd $CHTML #> mkdir ../doc #> for i in *.html; do lynx -dump $i >
> ../doc/${i%html}doc; done #> bash makeman.sh
> 
> That's good enough for me.
> 
> Regards,
> Tim
> 
> On 11/15/2013 03:46 PM, Martyn Winn wrote:
> > Many, many years ago, the man pages used to be nroff-formatted .1
> > files. We converted these to html files, and used lynx to
> > automatically generate ASCII .doc files which could be used as man
> > pages. AFAIK this is still the case.
> >
> > I mention this in case anyone wants to get nostalgic about
> > nroff/groff/troff ...
> >
> > Martyn
> >
> >> -Original Message- From: CCP4 bulletin board
> >> [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Evans Sent: 15
> >> November 2013 14:37 To: ccp4bb Subject: Re: [ccp4bb] ccp4 man-pages
> >>
> >> AFAICS the .doc files look as if they were auto-generated from the
> >> .html files in 6.3.0. Certainly the only documentation I have
> written
> >> for Pointless and Aimless is in html
> >>
> >> Phil
> >>
> >> On 15 Nov 2013, at 14:33, "Edward A. Berry" 
> >> wrote:
> >>
> >>>> (assuming of course the .doc files aren't also missing).
> >>>
> >>> CDOC: Undefined variable. [berry@sbserv ~]$ ls $CCP4/doc ls:
> >>> cannot access /sw/lnx/ccp4-6.4.0/doc: No such file or directory
> >>>
> >>> I second the request for continued man pages and .doc files
> >>>
> >>> Ian Tickle wrote:
> >>>> I agree completely with Tim: I use 'man' (or 'info' for gfortran &
> >>>> the like) all the time - but then I'm a die-hard
> >>>> command-liner/shell-scripter who never
> >> uses
> >>>> ccp4i!  I haven't got around to installing 6.4 yet but if & when I
> >> do
> >>>> & I find the man pages missing as Tim says I'll probably copy over
> >>>> the ones from 6.3 - even though they're maybe now a bit out of
> >>>> date,
> >> it's better than no man pages!  ... or maybe better would be
> >> something like:
> >>>>
> >>>> alias manc 'less $CDOC/\!^.doc'
> >>>>
> >>>> (assuming of course the .doc files aren't also missing).
> >>>>
> >>>> ... or this looks promising:
> >>>> ftp://jaguar.ncsl.nist.gov/current_docs/sctk-1.2/doc/html2man.pl
> >>
> >>>>
> (haven't tried it though).
> >>>>
> >>>> Cheers
> >>>>
> >>>> -- Ian
> >>>>
> >>>>
> >>>> On 15 November 2013 09:48, Tim Gruene  >>>> <mailto:t...@shelx.uni-ac.gwdg.de>>
> >>>> wrote:
> >>>>
> > Dear all,
> >
> > I am sorry about this 'double' post, but I had no reply on
> >>> ccp4bb-dev
> > within about three weeks.
> >
> > I wonder if I was the only one using the ccp4 man-pages. They
> >>> were
> > available until ccp4-6.3 but seem to be absent in the latest
> >>> version.
> >
> > I find them utterly handy, much faster than locating the
> > html-documentation through a web-browser and they probably do not
> >>> take
> > up much space.
> >
> > So I hope to get some votes for redistributing the man-pages
> >>> through
> > the ccp4bb.
> >
> > Best, Tim
> >
> >>>>
> >>>>
> >
> 
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
> 
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Icedove - http://www.enigmail.net/
> 
> iD8DBQFShjcLUxlJ7aRr7hoRAht2AKDPaMcvpZYm1rOhrSjaxHGIzlV1pgCfdVh3
> YcONbO4cGNucEcqacLn/1rc=
> =KZas
> -END PGP SIGNATURE-

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Re: [ccp4bb] ccp4 man-pages

[Martyn Winn]

Many, many years ago, the man pages used to be nroff-formatted .1 files. We 
converted these to html files, and used lynx to automatically generate ASCII 
.doc files which could be used as man pages. AFAIK this is still the case.

I mention this in case anyone wants to get nostalgic about nroff/groff/troff ...

Martyn

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Phil Evans
> Sent: 15 November 2013 14:37
> To: ccp4bb
> Subject: Re: [ccp4bb] ccp4 man-pages
> 
> AFAICS the .doc files look as if they were auto-generated from the
> .html files in 6.3.0. Certainly the only documentation I have written
> for Pointless and Aimless is in html
> 
> Phil
> 
> On 15 Nov 2013, at 14:33, "Edward A. Berry"  wrote:
> 
> > > (assuming of course the .doc files aren't also missing).
> >
> > CDOC: Undefined variable.
> > [berry@sbserv ~]$ ls $CCP4/doc
> > ls: cannot access /sw/lnx/ccp4-6.4.0/doc: No such file or directory
> >
> > I second the request for continued man pages and .doc files
> >
> > Ian Tickle wrote:
> >> I agree completely with Tim: I use 'man' (or 'info' for gfortran &
> >> the like) all the time
> >> - but then I'm a die-hard command-liner/shell-scripter who never
> uses
> >> ccp4i!  I haven't got around to installing 6.4 yet but if & when I
> do
> >> & I find the man pages missing as Tim says I'll probably copy over
> >> the ones from 6.3 - even though they're maybe now a bit out of date,
> it's better than no man pages!  ... or maybe better would be something
> like:
> >>
> >> alias manc 'less $CDOC/\!^.doc'
> >>
> >> (assuming of course the .doc files aren't also missing).
> >>
> >> ... or this looks promising:
> >> ftp://jaguar.ncsl.nist.gov/current_docs/sctk-1.2/doc/html2man.pl
> (haven't tried it though).
> >>
> >> Cheers
> >>
> >> -- Ian
> >>
> >>
> >> On 15 November 2013 09:48, Tim Gruene  >> > wrote:
> >>
> >>-BEGIN PGP SIGNED MESSAGE-
> >>Hash: SHA1
> >>
> >>Dear all,
> >>
> >>I am sorry about this 'double' post, but I had no reply on
> ccp4bb-dev
> >>within about three weeks.
> >>
> >>I wonder if I was the only one using the ccp4 man-pages. They
> were
> >>available until ccp4-6.3 but seem to be absent in the latest
> version.
> >>
> >>I find them utterly handy, much faster than locating the
> >>html-documentation through a web-browser and they probably do not
> take
> >>up much space.
> >>
> >>So I hope to get some votes for redistributing the man-pages
> through
> >>the ccp4bb.
> >>
> >>Best,
> >>Tim
> >>
> >>- --
> >>- --
> >>Dr Tim Gruene
> >>Institut fuer anorganische Chemie
> >>Tammannstr. 4
> >>D-37077 Goettingen
> >>
> >>GPG Key ID = A46BEE1A
> >>
> >>-BEGIN PGP SIGNATURE-
> >>Version: GnuPG v1.4.12 (GNU/Linux)
> >>Comment: Using GnuPG with Icedove - http://www.enigmail.net/
> >>
> >>iD8DBQFShe4AUxlJ7aRr7hoRAh5qAJ4sHMCDcv1QfVUEmBCzLzNTbqkdvQCfRe4Q
> >>RKQR1yeSfLPRFmt/C0RVxWA=
> >>=U9wW
> >>-END PGP SIGNATURE-
> >>
> >>

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[ccp4bb] Position available in biomolecular simulation

[Martyn Winn]

Hi all,

We have an opening for a computational scientist within my group at Daresbury 
(Cheshire, UK) to provide core support to the EPSRC-funded High-End Computing 
(HEC) Consortium in biomolecular simulation.

The post will support the consortium through porting and optimisation of a 
variety of biomolecular simulation codes, with a focus on high performance 
computing. The post will also contribute to the development of a HEC toolkit 
designed to lower the barrier to the use of HEC resources. There may also be 
opportunities to contribute to science projects within the Daresbury group. 
Candidates must have strong programming skills and some experience of HEC 
systems.

Further details are available at 
http://www.topcareer.jobs/Vacancy/irc108813_3575.aspx and you should also apply 
through that site (by 30th Sept). I am happy to take informal enquiries.

Cheers
Martyn

*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*



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Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

[Martyn Winn]

Hi,

There have been many discussions along these lines over the years.  The problem 
is understood well. The favoured solution is the use of mmCIF (as posted 
several times on the BB). But I would rather leave it to those officially 
involved to comment on the pros and cons. On the practical side, pdbcur will 
work equally well with mmCIF files.

Cheers
Martyn

*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk<mailto:martyn.w...@stfc.ac.uk>   Skype: 
martyn.winn
*


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk 
Kostrewa
Sent: 02 September 2013 09:38
To: ccp4bb
Subject: Re: [ccp4bb] Fractional coordinate shift with two-character chain 
names?

Dear Martyn, Pavel and other interested,

I think, an official extension by the PDB to two characters for the chain names 
and 5 digits for residues would really help. I'm currently working on a 
structure with 6x15 chains (through NCS) - it is huge and only a few programs 
can handle this by extending the PDB format.
The last PDB format revision 
3.3<http://www.wwpdb.org/documentation/format33/sect9.html#ATOM> still only 
allows one character for the chain name and four digits for the residue number.
More bigger structures will be published in the future and an official 
human-readable extended PDB format would really help.

Cheers,

Dirk.

Am 30.08.13 18:14, schrieb MARTYN SYMMONS:
Hold your horsemen!
Does not this option save us from 'formatagedon'?
We currently only have single letters or numbers for chains. But we could 
easily agree to switch to double letters. And long chains can be a sequence of 
letter number permutations such as A1, A2, A3 etc (actually I notice single 
numbers are allowed for the PDB - although are deprecated until all the letters 
have been used).
We could allow the first character to be a number as well - so 11 12 13 as a 
valid sequence.for a single polymer.
Conversely we could expand the atom identifier to include letters as is the 
case with most computing identifiers - however not many programs seem to pay 
attention to the atom 'numbers' in any case.

Cheers
  Martyn

Martyn Symmons (not Winn)
Cambridge


From: Dirk Kostrewa 
<mailto:kostr...@genzentrum.lmu.de>
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Sent: Friday, 30 August 2013, 15:36
Subject: Re: [ccp4bb] Fractional coordinate shift with two-character chain 
names?

Hi Martyn,

excellent - this worked!

Many thanks!

Cheers,

Dirk.

Am 30.08.13 16:04, schrieb Martyn Winn:
> IIRC the CCP4 library (i.e. mmdb) can handle 2-character chain names. There 
> may be something specific in pdbset which interferes. You can try pdbcur as 
> an alternative. Something like:
>
> pdbcur xyzin toxd_AA.pdb xyzout toxd_out.pdb < translate * frac 0 0.2 0
> end
> eof
>
> I just tried it on a little example, and it works for me.
>
> Cheers
> Martyn
>
>> -Original Message-
>> From: CCP4 bulletin board 
>> [mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of
>> Dirk Kostrewa
>> Sent: 30 August 2013 14:41
>> To: ccp4bb
>> Subject: [ccp4bb] Fractional coordinate shift with two-character chain
>> names?
>>
>> Dear CCP4ers,
>>
>> I want to apply a fractional coordinate shift along a polar b-axis with
>> coordinates that have non-standard two-character chain names, such as
>> "AA", "AB", and so forth. Unfortunately, neither the old USF moleman2
>> nor the actual CCP4 pdbset can handle these chain names. To my
>> knowledge, only COOT and PHENIX can cope with them.
>> Before I start writing my own little jiffy, is there a quick way to use
>> COOT or PHENIX to apply a fractional coordinate shift, or could you
>> tell me, which other program I can use in this special case?
>>
>> Best regards,
>>
>> Dirk.
>>
>> --
>>
>> ***
>> Dirk Kostrewa
>> Gene Center Munich
>> Department of Biochemistry
>> Ludwig-Maximilians-Universität München
>> Feodor-Lynen-Str. 25
>> D-81377 Munich
>> Germany
>> Phone: +49-89-2180-76845
>> Fax: +49-89-2180-76999
>> E-mail:kostr...@genzentrum.lmu.de<mailto:kostr...@genzentrum.lmu.de>
>> WWW:www.genzentrum.lmu.de<http://www.genzentrum.lmu.de>
>> ***

--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-

Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

[Martyn Winn]

IIRC the CCP4 library (i.e. mmdb) can handle 2-character chain names. There may 
be something specific in pdbset which interferes. You can try pdbcur as an 
alternative. Something like:

pdbcur xyzin toxd_AA.pdb xyzout toxd_out.pdb < -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Dirk Kostrewa
> Sent: 30 August 2013 14:41
> To: ccp4bb
> Subject: [ccp4bb] Fractional coordinate shift with two-character chain
> names?
> 
> Dear CCP4ers,
> 
> I want to apply a fractional coordinate shift along a polar b-axis with
> coordinates that have non-standard two-character chain names, such as
> "AA", "AB", and so forth. Unfortunately, neither the old USF moleman2
> nor the actual CCP4 pdbset can handle these chain names. To my
> knowledge, only COOT and PHENIX can cope with them.
> Before I start writing my own little jiffy, is there a quick way to use
> COOT or PHENIX to apply a fractional coordinate shift, or could you
> tell me, which other program I can use in this special case?
> 
> Best regards,
> 
> Dirk.
> 
> --
> 
> ***
> Dirk Kostrewa
> Gene Center Munich
> Department of Biochemistry
> Ludwig-Maximilians-Universität München
> Feodor-Lynen-Str. 25
> D-81377 Munich
> Germany
> Phone:+49-89-2180-76845
> Fax:  +49-89-2180-76999
> E-mail:   kostr...@genzentrum.lmu.de
> WWW:  www.genzentrum.lmu.de
> ***

[ccp4bb] 2 positions available for software developers in cryoEM

[Martyn Winn]

Dear All,

I have 2 positions available for software developers in cryoEM:

1) A developer to work alongside Chris Wood on the CCP-EM project. The post 
will support a number of software development projects (see e.g. 
http://www.ccpem.ac.uk/ccpem_projects.php), as well as providing general 
community support. 
2) A developer to work on Work Package 9 of the BioMedBridges grant 
(http://www.biomedbridges.eu/), concerned with developing a database of volumes 
with associated tools, in collaboration with developers at the EBI. 

We are looking for talented developers of scientific software. While knowledge 
of cryoEM and structural biology would be an advantage, applicants from other 
backgrounds are welcomed if you can demonstrate an ability to learn and a 
flexibility in approach. The projects are collaborative in nature, so you must 
be a good communicator and be able to work as part of a team.

The posts are located at the Research Complex at Harwell 
(http://www.rc-harwell.ac.uk/), within the group of Martyn Winn in the 
Scientific Computing Department of STFC (http://www.stfc.ac.uk/scd/), and 
alongside the core team of CCP4. The Research Complex is located on the Harwell 
Science and Innovation Campus, adjacent to the Diamond synchrotron and provides 
an exciting multi-disciplinary work environment, including many relevant 
structural biology groups.

Applications need to be made via the TopCareer site (see links on 
http://www.ccpem.ac.uk/positions.php) and informal enquiries can be made to me.

Cheers
Martyn


*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*



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Re: [ccp4bb] Why the name "aimless"

[Martyn Winn]

I think Phil saw something nasty in the woodshed ...

HTH
Martyn

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Roberto Battistutta
> Sent: 02 May 2013 11:07
> To: ccp4bb
> Subject: [ccp4bb] Why the name "aimless"
> 
> Hi everyone,
> just a curiosity, why the name "aimless" for the recent data reduction
> and analysis program in CCP4? You know, my students are curious ...
> Thank you,
> Roberto.
> 
> 
> Roberto Battistutta
> Associate Professor
> Department of Chemistry
> University of Padua
> via Marzolo 1, 35131 Padova - ITALY
> tel. +39.049.827.5262
> fax. +39.049.827.5829
> roberto.battistu...@unipd.it
> www.chimica.unipd.it/roberto.battistutta/
> VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129
> Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it

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[ccp4bb] Questionnaire on shape/volume fitting in structural biology

[Martyn Winn]

Dear Colleagues,

PDBe and STFC are developing a web service as part of the BioMedBridges project 
(http://www.biomedbridges.eu/workpackages/wp9) that will enable the EMDB and 
PDB archives to be searched on the basis on 3D volumetric shape matching rather 
than solely on the basis of metadata and/or coordinate models. For example, 
users will be able to upload a 50S ribosome map and retrieve aligned maps of 
other ribosomes in the archives. We will also use the service to automatically 
fit and segment existing entries when new entries are deposited that share 
common components, e.g. a newly deposited ribosomal protein will be fitted into 
ribosomal maps in the PDB/EMDB and the resulting segmentations will be made 
publicly available. In due course, the service may be extended to other 
volumetric data, such as from SAXS or soft X-ray tomography.

We are taken our first baby steps in this project and need your help to avoid 
reinventing the wheel - we want to use existing software wherever possible! We 
would like to know what tools and in which context you use fitting software, 
including fitting atomic coordinates in a volume, fitting EM single particle 
volumes in tomograms, comparing an EM volume with a SAXS envelope, and 
comparing a EM single particle volume with a sub-tomogram average.

Please take a moment to fill in our questionnaire on shape/volume fitting in 
structural biology following this link 
http://www.surveymonkey.com/s/BioMedBridgesShapeMatchingSurvey
to Survey Monkey.  We plan to publish an anonymized summary of the survey on 
the BioMedBridges web site.

Kind Regards,
Ingvar Lagerstedt & Ardan Patwardhan, PDBe and Martyn Winn, STFC



*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*




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[ccp4bb] CCPBioSim workshop on MD and Annual Conference

[Martyn Winn]

Dear All,

CCPBioSim are once again running a 1-day workshop covering the basics of 
setting up Molecular Dynamics simulations for biological systems. The workshop 
is on Wednesday 20th March 2013 at the Unilever Centre for Molecular 
Informatics, University of Cambridge. The deadline for applications is Friday 
8th March. Further details at:
http://www.ccpbiosim.ac.uk/?q=workshops/2ndSetupSimulation

Also, a reminder that the closing date for registrations for the Annual 
Conference of CCPBioSim is today. If there are any last minute registrations, 
please register asap and/or let me know. Further details at:
http://www.ccpbiosim.ac.uk/?q=annualconfs/conf2013

Cheers
Martyn

*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*




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[ccp4bb] Register now for the CCP-BioSim Conference: Frontiers of Biomolecular Simulation

[Martyn Winn]

Dear All, 

Registration is now open for the second annual meeting of CCP-BioSim "Frontiers 
of Biomolecular Simulation" at the University of Nottingham, Monday 25th to 
Wednesday 27th March 2013. The meeting is open to all - registration provides 
FREE membership of CCP-BioSim.

We have an impressive list of invited speakers: Alessio Ciulli (Cambridge), 
Gianni De Fabritiis (Barcelona), Philippe Hünenberger (ETH Zurich), Ruth 
Nussinov (Tel Aviv/NCI), Lars Schaefer (Frankfurt), Nigel Scrutton 
(Manchester), and Joanna Trylska (Warsaw).

Thanks to support from EPSRC and MGMS, we have been able to keep costs low; the 
registration fee: £50/75 (students/non-students) includes refreshments and 
conference dinner. On-site accommodation is available separately. 

If you are interested in presenting a short talk and/or poster REGISTER NOW - 
DEADLINE IS THE 21ST JANUARY. There are bursaries from the Molecular Graphics 
and Modelling Society for selected junior researchers.

For full details and to register, see: http://www.ccpbiosim.ac.uk


*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*




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[ccp4bb] Instruct Biennial Meeting 22-24th May - Registration Open

[Martyn Winn]

Dear all,

Registration for the first Instruct Biennial Structural Biology Meeting taking 
place on the 22-24th May, 2013, at EMBL Heidelberg Advance Training Centre is 
now open. Registration for the conference is free. The meeting will showcase 
integrative structural biology and its impact on biological research and 
development. Confirmed speakers include:

So Iwata, Elena Conti, Tim Springer, Carol Robinson, David Eisenberg, Dinshaw 
Patel, Roger Sunahara, Thomas Muller Reichert and Wolfgang Baumeister.

The talks will represent recent structural biology highlights, emerging methods 
and technologies and results of biomedical importance. A special session, 
jointly organised with Euro-Bioimaging, will focus on the bridge between 
structural and cell biology provided by recent developments in electron, light 
and X-ray microscopy. The position of Instruct in the wider context of 
integrated European infrastructure will also be presented.

Young scientists interested in gaining a broader understanding of structural 
biology and its community are especially encouraged to attend. Four abstracts 
from participants will be chosen to give talks at the meeting.

For more details, and to register, visit 
http://www.structuralbiology.eu/content/instruct-biennial-structural-biology-meeting

Best wishes,
The Instruct Operations Team

*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*



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[ccp4bb] two positions available in computational electron cryo-microscopy

[Martyn Winn]

See http://www.ccpem.ac.uk/positions.php

The Research Complex at Harwell, Oxfordshire, UK hosts a growing number of 
computational scientists supporting a wide range of structural biology 
research. We have two vacancies for enthusiastic scientists with experience of 
computational methods to join the group. You will join one of two projects, 
both concerned with exploiting the recent growth in the application of electron 
cryo-microscopy (cryo-EM) to structural and cellular biology. 

Post 1: The European infrastructure project BioMedBridges 
(http://www.biomedbridges.eu) is constructing an e-infrastructure to allow 
interoperability between data and services in the biological, medical, 
translational and clinical domains. This post will contribute to Work Package 9 
of Biomedbridges, which is a Use Case illustrating sharing of cryoEM data 
between structural biologists and biological database providers. You will 
create software for analysing, comparing and annotating cryoEM maps, in 
collaboration with developers at the EBI.

Post 2: We seek an experienced scientist with an interest in software 
development, to work alongside the current project developer, on the 
Collaborative Computational Project for cryoEM (http://www.ccpem.ac.uk). You 
will be responsible for developing the CCP-EM software suite, in collaboration 
with application developers in the consortium, as well as developing and 
promoting community standards.

Both posts will be located at the Research Complex at Harwell, within the 
Computational Biology group of Martyn Winn in the Scientific Computing 
Department of STFC. Further information is available online (see 
http://www.ccpem.ac.uk/positions.php and links to TopCareer site), and informal 
enquiries may be made to Martyn Winn martyn.w...@stfc.ac.uk

*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*



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[ccp4bb] 2013 CCP-BIOSIM ANNUAL CONFERENCE: Frontiers of Biomolecular Simulation

[Martyn Winn]

Registration is now open for the second annual meeting of CCP-BioSim "Frontiers 
of Biomolecular Simulation" at the University of Nottingham, Monday 25th to 
Wednesday 27th March 2013. The meeting is open to all - registration provides 
free membership of CCP-BioSim.

* Invited Speakers: Alessio Ciulli (Cambridge), Gianni De Fabritis (Barcelona), 
Philippe Hünenberger (ETH Zurich), Ruth Nussinov (Tel Aviv/NCI), Lars Schaefer 
(Frankfurt), Nigel Scrutton (Manchester), Joanna Trylska (Warsaw).

* Deadline for receipt of applications to present short talks and/or posters: 
31st December. Bursaries from the Molecular Graphics and Modelling Society for 
selected junior researchers.

* Registration fee: £50/75 (students/non-students) includes refreshments and 
conference dinner. On-site accommodation available separately.

* For full details and to register, see: www.ccpbiosim.ac.uk


*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.w...@stfc.ac.uk   Skype: martyn.winn
*




-- 
Scanned by iCritical.

Re: [ccp4bb] Crystallography on BBC Radio 4 next week

[Martyn Winn]

I'd just like to comment that In Our Time is usually pretty good. I caught the 
end of this morning's program on the Borgias. After hearing about murder, 
nepotism and incest, it was a bit disorientating to hear Melvyn announce 
crystallography as the next subject :)

m

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Peter Keller
> Sent: 22 November 2012 13:52
> To: ccp4bb
> Subject: Re: [ccp4bb] Crystallography on BBC Radio 4 next week
> 
> Dear all,
> 
> I have had several queries about this off-list, so here are some
> clarifications.
> 
> I don't know if Melvyn Bragg is related to WL and WH Bragg. I doubt it,
> but if he is maybe he will say. (Bragg is a fairly common name in
> English.)
> 
> The normal subject matter of "In Our Time" is humanities-based (i.e.
> art, history, philosophy etc.), but they deal with scientific or
> mathematical subjects occasionally.
> 
> There are two live broadcasts, at 09:00 and 21:30 UK time. The later
> one
> is a shortened version (edited from about 42 mins to about 28), so
> better to listen to the earlier one if you can.
> 
> There are three options for listening other than the terrestrial radio
> broadcast. All should work outside the UK (restrictions on using the
> BBC
> iPlayer overseas mostly apply only to television, or on the radio to
> certain special broadcasts such as some sporting events).
> 
> (i) Live on the internet at the times above: go to the programme page
> at
>  and click on the "LISTEN"
> icon (with a picture of a small loudspeaker) towards the upper right of
> the page.
> 
> (ii) Using iPlayer after the second broadcast has finished. Go to the
> programme page at  and click
> on the "Listen now" button on the left of the picture illustrating the
> programme. In principle this should become available within a few
> minutes of the end of the second broadcast (i.e. soon after 22:00 UK
> time), but sometimes there is a longer delay of up to an hour. It won't
> expire, so you can always listen on another day.
> 
> (iii) Download a podcast in mp3 format from
> . This will become available
> sometime after the second broadcast has finished, but it could be a day
> or two afterwards. These podcasts also don't expire or disappear: you
> can download them years after the original broadcasts.
> 
> Options (ii) and (iii) will get you the full rather than the shortened
> version of the programme.
> 
> Regards,
> Peter.
> 
> On Thu, 2012-11-22 at 10:30 +, Peter Keller wrote:
> > Dear all,
> >
> > On Thursday next week, the BBC radio program "In Our Time" will be
> > discussing the history of crystallography. The link to the program is
> > . Unfortunately, it doesn't
> say
> > who the guests are, but they usually manage to find people with
> something
> > interesting to say, even if the presenter Melvyn Bragg's grasp of
> scientific
> > material isn't always that great.
> >
> > I think that from outside the UK it is possible to listen live from
> the link
> > above, and that a day or two after the broadcast a podcast will be
> available
> > to download from .
> >
> > Regards,
> > Peter.
> >
> 
> --
> Peter Keller Tel.: +44 (0)1223
> 353033
> Global Phasing Ltd., Fax.: +44 (0)1223
> 366889
> Sheraton House,
> Castle Park,
> Cambridge CB3 0AX
> United Kingdom

[ccp4bb] CCP-BioSim workshop on Free energy methods for modelling of protein-ligand interactions

[martyn . winn]

This 1-day CCP-BioSim training workshop will introduce non-specialists to the 
use of free energy methods for modelling protein-ligand interactions and 
computing free energies of binding. It is aimed at postgraduate students and 
early-stage career researchers. The molecular simulation program ProtoMS 
(http://www.protoms.org) will be used. Instructors are Julien Michel 
(Edinburgh), Christopher Woods (Bristol), Michael Bodnarchuk (Southampton), 
Samuel Genheden (Southampton).

The workshop will take place on Wednesday, 21st November 2012 at the School of 
Chemistry, University of Southampton. Registration is free, but places are 
limited to 35. Further details can be found at:
http://www.ccpbiosim.ac.uk/?q=workshops/1stFreeEnergy

Cheers
Martyn

--
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***




-- 
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[ccp4bb] Senior computational scientist required for CCP-EM, Harwell, UK (IRC50666)

[martyn . winn]

The CCP-EM project aims to provide computational support for scientists and 
software developers using electron cryo-microscopy for structural biology, by 
analogy with similar successful projects in macromolecular crystallography 
(CCP4) and biological nuclear magnetic resonance spectroscopy (CCPN).

The CCP-EM project is now underway, with the involvement of scientists from 
several labs in the UK. We seek an experienced scientist with an interest in 
software development, to work alongside the current project developer. You will 
be responsible for developing the CCP-EM software suite, in collaboration with 
application developers in the consortium. You will also help to apply community 
standards for cryo-EM data, and provide user support and training.

You will be an experienced developer of scientific software. You will have 
research experience in structural biology or bioinformatics, with a good 
publication record. Direct experience of cryo-EM would be a distinct advantage, 
but may not be essential if you can demonstrate some knowledge and an ability 
to learn. The project is collaborative in nature, so you must be a good 
communicator and be able to work as part of a team.

The core group of CCP-EM is based at the Research Complex at Harwell, alongside 
the core group of CCP4, but the postholders will be expected to travel 
throughout the UK and interact with international groups to support the 
collaboration. Informal enquiries may be made to Martyn Winn 
martyn.w...@stfc.ac.uk

The post is fixed-term until August 2015, and the salary is £33780 - £37534 
dependent on experience.

Applications are handled by the RCUK Shared Services Centre; to apply please 
visit our job board at www.topcareer.jobs to view the full job description and 
person requirements and complete an online application. If you are unable to 
apply online please contact us on 01793 867003 quoting reference IRC50666.

Closing date: 24 Sep 2012



--
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***




-- 
Scanned by iCritical.

Re: [ccp4bb] brix/mrc to ccp4 (was Re: [ccp4bb] AW: [ccp4bb] Postdoctoral position - University of Edinburgh)

[martyn . winn]

Indeed, the intention is that .mrc and CCP4 .map are identical. There have been 
some problems over the years, which I would call bugs, leading to apparent 
incompatibility. I'd be interested in any specific cases of non-conforming 
software (i.e. if there are some .mrc files which CCP4 programs can't read 
(simplest test is "mapdump MAPIN foo.mrc"), I'd need to know which version of 
which program generated it).

Cheers
Martyn

--
***
*     *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***



> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Pete Meyer
> Sent: 25 June 2012 15:32
> To: ccp4bb
> Subject: [ccp4bb] brix/mrc to ccp4 (was Re: [ccp4bb] AW: [ccp4bb]
> Postdoctoral position - University of Edinburgh)
> 
> I don't know of anything directly within CCP4 - but mrc format is
> almost
> identical to ccp4 map format.  You could try using the mrc version as
> ccp4 and see if it works.  If not, upsalla mapman will convert brix to
> ccp4.
> 
> Pete
> 
> Froehlich, Chris wrote:
> > Dear colleagues,
> >
> > is there any program enclosed in CCP4 to convert a *.brix file or a
> *.mrc file into a CCP4.map file?
> > If not, is there any other way to do so?`
> >
> > Alle the best,
> > Chris
> >
> >
> > DIPL.-ING. CHRIS FRÖHLICH
> > Crystallography Dept. | Daumke group
> > Max-Delbrück-Centre for Molecular Medicine (MDC)
> > Robert-Rössle-Str. 10
> > 13125 Berlin-Buch
> > Lab: +49(0)30-9406-3263
> > Office: +49(0)30-9406-3275
> > Fax: +49(0)30-9406-3814
> >
> > www.mdc-berlin.de/daumke<http://www.mdc-berlin.de/daumke>
> >
> >

[ccp4bb] CCP-BioSim workshop on QM/MM methods for modelling enzyme-catalysed reactions

[martyn . winn]

CCP-BioSim workshop on QM/MM methods for modelling enzyme-catalysed reactions
School of Chemistry, University of Bristol, UK
Tuesday July 17th 2012

This practical workshop will introduce combined quantum mechanics/molecular 
mechanics (QM/MM) methods and their application to modelling enzyme-catalysed 
reactions. It will involve hands-on use of QM/MM methods, in particular using 
the CHARMM program, and their application to modelling a reaction within an 
enzyme. No prior experience of simulations or QM/MM methods is required; the 
workshop is suitable for non-specialists. 

Registration is free to academic researchers and students. Places are limited. 
Lunch will be provided. 
Registration is via: 

<https://eventbooking.stfc.ac.uk/news-events/ccpbiosim-training-workshop-qmmm-methods-for-modelling-enzyme-catalysed-reactions>

Cheers 
Martyn

P.S. "Sorry for the non-CCP4 post"

--
***
* *
*       Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] Covert Structure Factor to mtz

[martyn . winn]

But that's not what Paul said. I am sure we all agree the information _should_ 
be there, but I took Paul to mean that it _is_ there.

If I look at PDBe for 2gs7, go to Downloads and Structure Factors, then the 
cell and symmetry is _not_ there.
If I go to RCSB, and click on Structure Factors on the RHS, same file, and 
cell/symm is _not_ there.

1f9j is another example. Really, there are lots. I am not going to report them 
all...

There was also (last time I looked) a number of entries that had a CRYST1 card 
included in a cif comment section.

Cheers
Martyn

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jon Agirre
Sent: 18 May 2012 09:34
To: ccp4bb
Subject: Re: [ccp4bb] Covert Structure Factor to mtz

I completely agree with Paul. That information could even be enclosed by two 
commentary sections (i.e. '# Added by wwPDB mm-dd- hh:mm' and 
'') to highlight the changes.

Jon
2012/5/18 Paul Emsley 
mailto:paul.ems...@bioch.ox.ac.uk>>
On 17/05/12 20:16, martyn.w...@stfc.ac.uk wrote:
Reflection cif files from the PDB do not always have cell and symmetry 
information in them, particularly the older ones, and it sounds like this is 
your case.

My understanding is that these days they should have - and if you find such 
examples, they should be reported to the wwPDB authorities.

Paul.



--
Dr. Jon Agirre
Postdoctoral Scientist - Protein and
Virus X-ray Crystallography Group
Biophysics Unit (CSIC-UPV/EHU)
+0034946013357

Re: [ccp4bb] Covert Structure Factor to mtz

[martyn . winn]

Reflection cif files from the PDB do not always have cell and symmetry 
information in them, particularly the older ones, and it sounds like this is 
your case.
In that case, you need to manually copy the cell information from the PDB web 
page into the ccp4i interface before running.

HTH
Martyn

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Uma Ratu
Sent: 17 May 2012 20:04
To: ccp4bb
Subject: [ccp4bb] Covert Structure Factor to mtz

Dear All:

I try to convert the .cif files (the structure factor files from PDB) to mtz 
file.

>From ccp4i, I chose "convert to/modify/extend mtz" for this purpose.

But program keep complanining:

"no cell information in keywords or files"

I open the .cif file in text, and could not find any information about cell 
information.

Is there a easy way to convert the .cif file from PDB to mtz?

Thank you for advice

Uma

Re: [ccp4bb] Off topic about program for multiple protein sequence alignment

[martyn . winn]

Certainly different programs and different scoring matrices will give different 
answers. There is not necessarily a correct answer either, just different 
educated guesses. With high sequence identity, the answers should be fairly 
consistent. As you reduce the sequence identity (i.e. as it gets more 
interesting) then the answers will vary more.

I think clustalw is generally considered to be one of the poorer multiple 
alignment programs these days (though I am sure opinions will vary here). By 
poor, I mean it struggles in the twilight zone of 25 - 30% seq identity, but is 
perfectly adequate for routine use. There are many other programs to choose 
from: probcons, mafft, TCoffee, Muscle, etc etc. In some tests of MrBUMP, we 
found some marginal cases that relied on using an alignment from probcons or 
mafft, rather than clustalw.

HTH
Martyn


> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Tim Gruene
> Sent: 15 May 2012 08:20
> To: ccp4bb
> Subject: Re: [ccp4bb] Off topic about program for multiple protein
> sequence alignment
> 
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Dear Donghui,
> 
> even within one program (clustalw) you would get different results by
> picking different weighting schemes (clustalx: Aligment->Alignment
> Parameter -> Multiple Alignment Parameter: BLOSUM, PAM, Gonnet...).
> 
> As with any software I would assume the developers know best what they
> are doing and recommend to stick to the defaults unless you know what
> you are doing.
> 
> Regards,
> Tim
> 
> On 05/15/12 08:02, wu donghui wrote:
> > Dear all,
> >
> > I want to know your suggestions about current protein sequence
> > alignment programs. It seems that different programs give different
> > alignment results such as from analysis of Clustal W and MULTALIN.
> > Thanks for any input or comments.
> >
> > Best regards,
> >
> > Donghui
> >
> 
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
> 
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
> 
> iD8DBQFPsgOYUxlJ7aRr7hoRArwKAKCqhK2012Ihnof7xjRzyao7GI8xpgCfZj/G
> VfD3ly3bmqycO0mX888oYfE=
> =7v6r
> -END PGP SIGNATURE-

[ccp4bb] reminder: CCP-EM positions now available

[martyn . winn]

 
A reminder that the deadline for these positions is this Friday (11 May 2012). 
If you have any questions, or problems with the application procedure, please 
contact me off-list.
Martyn

---

Dear Colleagues,

We have been awarded a Partnership grant by the MRC to provide computational 
support for UK scientists using electron cryo-microscopy for structural 
biology. One of the major aims is to create a Collaborative Computational 
Project, CCP-EM, by analogy with similar successful projects in macromolecular 
crystallography (CCP4) and biological nuclear magnetic resonance spectroscopy 
(CCPN). We seek two excellent and motivated computational scientists to support 
the Partnership grant and the CCP-EM project. These posts will have a wide 
variety of responsibilities, including writing community code, improving the 
useability of existing code, providing training, and supporting individual 
scientists. The first post will focus on technical aspects, building community 
tools and improving the programs available. The second post will focus more on 
the scientific requirements of the community. The posts are located at the 
Research Complex at Harwell (near Oxford), alongside the core group of CCP4, 
but the postholders will be expected to travel throughout the UK and interact 
with international groups to support the collaboration.

Applications must be made through the RCUK Shared Services recruitment portal 
https://ext.ssc.rcuk.ac.uk/ using the references IRC50385 and IRC50666. Further 
information is available there. Informal enquiries may be made to Martyn Winn 
(martyn.winn at stfc.ac.uk).

Best wishes,
Martyn Winn, Richard Henderson, Alan Roseman, Peter Rosenthal, Helen Saibil and 
Ardan Patwardhan

--
***
* * 
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   *
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] REFMAC Riding Hydrogens

[Martyn Winn]

7; as in 1997 [2]? Even though 1997 is probably a poor
> > estimation of the corresponding year...
> > 
> > Cheers,
> > Tim
> > 
> > 
> > [1] "On contribution of hydrogen atoms to X-ray scattering"
> > http://www.phenix-online.org/newsletter/
> > [2] http://shelx.uni-ac.gwdg.de/SHELX/shelx.pdf
> > 
> > On 03/05/2012 09:14 PM, Pavel Afonine wrote:
> > > Hi,
> > >
> > > On Mon, Mar 5, 2012 at 11:52 AM, Matthew Franklin
> > wrote:
> > >
> > >> Adding the riding hydrogens generally gives you some improvement
> > in R
> > >> factors even with a good quality (i.e. stereochemically correct)
> > model.
> > >>
> > >
> > > and here are the results of more or less systematic test that
> > prove this:
> > >
> > > see "On contribution of hydrogen atoms to X-ray scattering"
> > > here:
> > > http://www.phenix-online.org/newsletter/
> > >
> > > Pavel
> > >
> > - --
> > Dr Tim Gruene
> > Institut fuer anorganische Chemie
> > Tammannstr. 4
> > D-37077 Goettingen
> > 
> > GPG Key ID = A46BEE1A
> > -BEGIN PGP SIGNATURE-
> > Version: GnuPG v1.4.11 (GNU/Linux)
> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
> > 
> > iD8DBQFPVSXkUxlJ7aRr7hoRAm1TAJ9Hyfhkl3yhD5QSKw9I4RSK58m0fACgmlxk
> > YGILzeMam/3gQVmCeh0vQ8k=
> > =3m2J
> > -END PGP SIGNATURE-
> >  
> > 
> > 
> > 
> 
> Garib N Murshudov 
> Structural Studies Division
> MRC Laboratory of Molecular Biology
> Hills Road 
> Cambridge 
> CB2 0QH UK
> Email: ga...@mrc-lmb.cam.ac.uk 
> Web http://www.mrc-lmb.cam.ac.uk
> 
> 
> 
> 
> 

-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] Fw: [ccp4bb] CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ does not work

[Martyn Winn]

Yep, works for me too.

1w2i-sf.cif contains no pdbx entries. Did you perhaps first download the
mmcif format coordinate file? 

On the RCSB site, the "mmCIF File" are coordinates, and "Structure
Factor (text)" are reflections in mmCIF format.

Cheers
Martyn

On Wed, 2012-02-29 at 02:33 -0800, Dialing Pretty wrote:
> I just have it successfully done: 
> 
> 
> Import reflection file in mmCIF format and create MTZ file
> 
> In 1w2i-sf.cif
> 
> 
> 
> - Forwarded Message -
> From: Jayashankar 
> To: Dialing Pretty  
> Cc: CCP4BB@jiscmail.ac.uk 
> Sent: Wednesday, 29 February 2012 7:05 PM
> Subject: Re: [ccp4bb] CCP4i Reflection DataUtilities: Convert
> to/modify/extend MTZ does not work
> 
> 
> I face exactly the same problem. any advice in this regard would be
> greatful.
> 
> 
> S.Jayashankar 
> Research Student 
> Institute for Biophysical Chemistry
> Hannover Medical School 
> Germany.
> 
> 
> On Wed, Feb 29, 2012 at 2:58 AM, Dialing Pretty
>  wrote:
> 
> Dear All,
> 
> I want to use "CCP4i Reflection DataUtilities: Convert
> to/modify/extend MTZ" to change a RCSB mmCIF file into MTZ
> file.
> 
> It shows there are a lot of data name (related to _pdbx_.or
> something else) not present in dictionary, and shows CCP4I
> termination status 0 "child process excited anormally".
> 
> I am looking forward to getting a reply from you on how to
> solve the problem.
> 
> Cheers,
> 
> Dialing
> 
>  
>     
> 
> 
> 
> 
> 

-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ does not work

[Martyn Winn]

If you send me the PDB id that you are trying to convert, I can
investigate.

This issue has come up a few times recently on the BB - you can also try
searching the archives for advice.

The version of cif2mtz + dictionary in the forthcoming 6.3 should cope
with a wider range of cif files.

Cheers
Martyn

On Wed, 2012-02-29 at 10:05 +0100, Jayashankar wrote:
> I face exactly the same problem. any advice in this regard would be
> greatful.
> 
> 
> S.Jayashankar 
> Research Student 
> Institute for Biophysical Chemistry
> Hannover Medical School 
> Germany.
> 
> 
> On Wed, Feb 29, 2012 at 2:58 AM, Dialing Pretty
>  wrote:
> 
> Dear All,
> 
> I want to use "CCP4i Reflection DataUtilities: Convert
> to/modify/extend MTZ" to change a RCSB mmCIF file into MTZ
> file.
> 
> It shows there are a lot of data name (related to _pdbx_.or
> something else) not present in dictionary, and shows CCP4I
> termination status 0 "child process excited anormally".
> 
> I am looking forward to getting a reply from you on how to
> solve the problem.
> 
> Cheers,
> 
> Dialing
> 
>  
> 
> 
> 

-- 
*******
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

[ccp4bb] CCPBioSim workshop: How to set up a Protein Simulation

[Martyn Winn]

One of our sister CCPs, CCPBioSim, is running a one-day workshop on "How
to set up a Protein Simulation" on April 20th in Cambridge. It is aimed
at people new to biological molecular dynamics simulations, and may be
suitable for any crystallographers who want to have a go. It will use
the (free) MD package Gromacs. 

Further details and registration are at:
https://eventbooking.stfc.ac.uk/news-events/how-to-set-up-a-protein-simulation

Cheers
Martyn

-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

[Martyn Winn]

uble bond essentially becomes a single bond
> >> with 1.53 bond length.
> >>
> >> I need advise on the way I have run prodrg and the explanations for the 
> >> results.
> >> Is it common to observe such values? Or it is due to the alternating
> >> single and double bonds in this structure.
> >
> > Dear Shveta,
> >
> >   I'd like to follow up Ian Tickle's answer. A survey we carried out 
> > recently suggested  that up to 70% of ligand structures in the PDB had bond 
> > and bond angle errors that could have been removed by better choice of 
> > restraints (to be published). Although most of the errors found are small, 
> > some were very large (> 10 s.d. from mean).
> >
> >  The Mogul program (http://www.ccdc.cam.ac.uk/products/csd_system/mogul/) 
> > can be used to analyse the geometry of any feature in a 3D ligand model 
> > against data in the Cambridge Structural Database and is available to 
> > anyone who has access to the Cambridge Structural Database System. The 
> > GRADE dictionary generation software from Global Phasing uses Mogul 
> > information behind the scenes to generate bond and bond angle restraints. 
> > In addition ligand validation and restraint correction using Mogul will 
> > become available via COOT before too long. Finally you might like to know 
> > we are working with the PDB so that the geometry of ligand models can be 
> > validated on submission.
> >
> >  Regards
> > John
> >
> > Dr John W. Liebeschuetz
> > Research & Applications Manager
> > Cambridge Crystallographic Data Centre
> > 12 Union Rd., Cambridge CB2 1EZ, UK
> > T:  +44-(0)1223-762532
> > F:  +44-(0)1223-336033
> >
> >
> >
> > LEGAL NOTICE
> > Unless expressly stated otherwise, information contained in this
> > message is confidential. If this message is not intended for you,
> > please inform postmas...@ccdc.cam.ac.uk and delete the message.
> > The Cambridge Crystallographic Data Centre is a company Limited
> > by Guarantee and a Registered Charity.
> > Registered in England No. 2155347 Registered Charity No. 800579
> > Registered office 12 Union Road, Cambridge CB2 1EZ.
> 
> 
> 

-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

[ccp4bb] Course reminder: Computational methods for macromolecular phasing and refinement, 11-16th March 2012

[Martyn Winn]

A CECAM/CCP4 Workshop will take place at the Spanish CECAM node in
Zaragoza from 19:00 on March 11th to 20:00 on March 16th 2012. The
overall objective of this course is to provide an intensive practical
training in all computational aspects of macromolecular structure
elucidation by X ray diffraction techniques, for advanced graduate
students and postdoctoral researchers. We will provide a general
introduction as well as tutorials; confirmed speakers and tutors include
Andrew Leslie, Garib Murshudov, George Sheldrick, Isabel Uson, Jorge
Navaza, Bernhard Lohkamp, Eugene Krissinel, Andrey Lebedev, Gabor
Bunckozi, Judit Debreczeni and Philipp Heuser.

The workshop is primarily funded by the Zaragoza and Daresbury CECAM
nodes. Additional support is provided by CCP4 and the supercomputing
centre FCSC. See the course website:
http://www.z-cam.es/activity_participants.php?num=52

The number of 'students' will be limited to 28. Thanks to generous
support from the CECAM nodes, we are able to provide accommodation (2 to
a room) and some meals. Students are responsible for their own travel.
The closing date for applications is February 3rd 2012.

Application is via the Ask/Apply tab on the course web site. You should
include in the message your name, gender (for shared accommodation),
brief details of your academic qualifications and of your research
project, including (very briefly) results achieved so far as well as
problems with phasing and/or refinement, the name of your research
supervisor or other person who may be consulted if necessary. All this
information will be treated confidentially. Participants are encouraged
to bring their own data.

Martyn Winn
Isabel Uson
Garib Murshudov


-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] How to patch CCP4 cif2mtz so it can handle PDB entries with Map Coefficients

[martyn . winn]

Thanks for this. I have recently updated the CCP4-supplied dictionary to 
include standard mmCIF, exchange dictionary, plus extra CCP4 items. This will 
be in the next release.
I was about to update cif2mtz to recognise these extra columns. Will look at 
what you have done, may save me a job.

cif2mtz is based on the ccif library, which complains if you try to load a cif 
file which contains a non-dictionary item. I'm sure in the past I tried to find 
a way round this, and failed.

>From the user point of view, the mmcif file is ascii and you can hand-edit the 
>column item names. This is the get-out method if cif2mtz fails. Edit the item 
>name to something that is recognised.

Cheers
Martyn

--
***
* *
*       Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***



> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Oliver Smart
> Sent: 21 December 2011 14:40
> To: ccp4bb
> Subject: [ccp4bb] How to patch CCP4 cif2mtz so it can handle PDB
> entries with Map Coefficients
> 
> Some recently released PDB entries (for instance 3u57) have structure
> factor files that contain map coefficients. We think this is a really
> good
> idea because it means that final maps as interpreted by the
> crystallographer will then be archived and available.
> 
> But there is a problem converting such files to mtz with the current
> cif2mtz program; indeed we raised this on the bb in September:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;6be4044e.1109
> 
> To get around this we produced a quick-fix patch for cif2mtz that is
> available at:
> 
> http://www.globalphasing.com/buster/wiki/index.cgi?CCP4cif2mtzPatchToHa
> ndleMapCoefficients
> 
> 
> Regards,
> 
> Oliver
> 
> | Dr Oliver Smart |
> | Global Phasing Ltd., Cambridge UK   |
> | http://www.globalphasing.com/people/osmart/ |

[ccp4bb] Course announcement: Computational methods for macromolecular phasing and refinement, 11-16th March 2012

[martyn . winn]

A CECAM/CCP4 Workshop will take place at the Spanish CECAM node in Zaragoza 
from 19:00 on March 11th to 20:00 on March 16th 2012. The overall objective of 
this course is to provide an intensive practical training in all computational 
aspects of macromolecular structure elucidation by X ray diffraction 
techniques, for advanced graduate students and postdoctoral researchers. We 
will provide a general introduction as well as tutorials; confirmed speakers 
and tutors include Andrew Leslie, Garib Murshudov, George Sheldrick, Isabel 
Uson, Jorge Navaza, Bernhard Lohkamp, Eugene Krissinel, Andrey Lebedev, Gabor 
Bunckozi and Judit Debreczeni.

The workshop is primarily funded by the Zaragoza and Daresbury CECAM nodes. 
Additional support is provided by CCP4 and the supercomputing centre FCSC. See 
the course website:
http://www.z-cam.es/activity_participants.php?num=52

The number of 'students' will be limited to 28. Thanks to generous support from 
the CECAM nodes, we are able to provide accommodation (2 to a room) and some 
meals. Students are responsible for their own travel. The closing date for 
applications is February 3rd 2012.

Application is via the Ask/Apply tab on the course web site. You should include 
in the message your name, gender (for shared accommodation), brief details of 
your academic qualifications and of your research project, including (very 
briefly) results achieved so far as well as problems with phasing and/or 
refinement, the name of your reseach supervisor or other person who may be 
consulted if necessary. All this information will be treated confidentially. 
Participants are encouraged to bring their own data.

Martyn Winn
Isabel Uson
Garib Murshudov

Re: [ccp4bb] converting mmcif to mtz failure

[Martyn Winn]

Yes, the program does need the (binary) data file cif_mmdic.lib which is
created from the cif_mm.dic file.

This should be in the directory C:\CCP4-Packages\ccp4-6.2.0\lib and NOT
C:\CCP4-Packages\ccp4-6.2.0\lib\data as you have. 

Which suggests that the environment variable MMCIFDIC is set wrongly.
And if I look at my windows installation  mmm yes it is set wrong
and cif2mtz indeed fails. Edit it in system -> advanced -> environment
variables (or whatever ), restart ccp4i, and voila it works!

So sorry, this looks like a cock-up in the windows distribution :(

HTH
Martyn

On Tue, 2011-09-06 at 16:34 -0500, Jacob Keller wrote:
> Dear Crystallographers,
> 
> in trying to convert a mmcif to mtz, I get the logfile below. I looked
> in the directory, and there is a file cf_mm.dic, but this is
> presumably not the same as the similar .lib file. Any thoughts about
> this? Did the file somehow get lost? Also, I recently did this same
> conversion to another file without problems...
> 
> Jacob Keller
> 
> 
> 
> #CCP4I VERSION CCP4Interface 2.1.0
> #CCP4I SCRIPT LOG import
> #CCP4I DATE 06 Sep 2011  16:29:11
> #CCP4I USER 'UNKNOWN'
> #CCP4I PROJECT 3mgl
> #CCP4I JOB_ID 3
> #CCP4I SCRATCH C:/Ccp4Temp
> #CCP4I HOSTNAME chloe
> #CCP4I PID 2728
> 
>  
> 
> 
> 
>  ###
>  ###
>  ###
>  ### CCP4 6.2: cif2mtz  version 6.2 : 16/11/09##
>  ###
>  User: Jacob  Run date:  6/ 9/2011 Run time: 16:29:19
> 
> 
>  Please reference: Collaborative Computational Project, Number 4. 1994.
>  "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst.
> D50, 760-763.
>  as well as any specific reference in the program write-up.
> 
>  Data line--- title [No title given]
>  Data line--- symmetry P4212
> 
>  Spacegroup information obtained from library file:
>  Logical Name: SYMINFO   Filename:
> C:\CCP4-Packages\ccp4-6.2.0\lib\data\syminfo.lib
> 
>  Data line--- cell 90.91 90.91 65.21 90.0 90.0 90.0
>  Data line--- end
> >>>> CCIF signal CCIF_FOPEN (severity: SEVERE ERROR/FATAL) <<<<
>   (Raised in zzs_undump)
> Cannot open file C:\CCP4-Packages\ccp4-6.2.0\lib\data\cif_mmdic.lib for 
> reading!
> 
> ***
> * Information from CCP4Interface script
> ***
> The program run with command: cif2mtz HKLIN
> "C:/Users/Jacob/Desktop/structures/PDB_3mgl/3mgl-sf.cif" HKLOUT
> "C:/Ccp4Temp/3mgl_3_1_mtz.tmp"
> has failed with error message
> child process exited abnormally
> ***
> 
> 
> #CCP4I TERMINATION STATUS 0 "child process exited abnormally"
> #CCP4I TERMINATION TIME 06 Sep 2011  16:29:19
> #CCP4I MESSAGE Task failed
> 

-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] identifying hinges in flexible proteins

[Martyn Winn]

DynDom version 1.5 is part of the CCP4 suite. 
There is an interface for it under Program List.

Although Steve Hayward appears to have a new version DynDom3D which we
don't have. No idea if it would be better for your case.

HTH
Martyn

On Fri, 2011-08-26 at 11:28 +0200, Matthew BOWLER wrote:
> Dear Stephen,
>  I find DynDom very good (http://fizz.cmp.uea.ac.uk/dyndom/) 
> otherwise the morph server 
> (http://molmovdb.mbb.yale.edu/molmovdb/morph/) also performs similar 
> analysis, cheers, Matt.
> 
> 
> On 26/08/2011 11:25, Stephen Cusack wrote:
> > We have structures of two states of a large multi-domain protein in 
> > which domain
> > movements of up to 30 degrees are observed. Is there a programme 
> > available which
> > attempts to determine rigid-body units and hinge regions in an 
> > 'unbiased' way?
> > thanks for your suggestions,
> > Stephen Cusack
> >
> 

-- 
***
*     *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] Pyroglutamate in structure calculation

[Martyn Winn]

Although I am sure there are people here who can help you, I guess you
are looking for the ccpn list:
http://www.jiscmail.ac.uk/lists/ccpnmr.html

I think CcpNmr Analysis includes an interface to Aria, so I guess they
can help you.

Cheers
Martyn

On Tue, 2011-08-16 at 10:40 +0200, Justin Lecher wrote:
> Hi all,
> 
> I like to use Aria to calculate the structure of a short peptide with a
> pyroglutamate at the Nterminus. The assignment through analysis was easy
> using a PCA as Nterminal aminoacid in the sequence. But neither the
> creation of an aria project.xml through extendNMR nor a manual setup
> through aria GUI works. Both ways give an error related to an unknown
> amino acid.
> 
> Could someone please point me to the correct way to setup the run and
> calculate the structure? Where do I need to include the additional
> topa/para definitions?
> 
> 
> Thanks justin
> 
> 

-- 
***
*     *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] protein segments from pdb

[Martyn Winn]

If you mean what I think you mean, then use the SUMMarise option of
pdbcur. That gives output like:

 Chain "A" has 505 residues 
 in 7 spans: 1-305 307-500 711-711 716-716 719-719 721-722 730-730
 0 residues have alternative conformations
 Composition: ALA 23 ARG 23 ASN 36 ASP 24 
  CYS 34 CYH 0 GLN 21 GLU 30 
  GLY 38 HIS 11 ILE 29 LEU 44 
  LYS 32 MET 8 PHE 17 PRO 21 
  SER 36 THR 28 TRP 5 TYR 13 
  VAL 26 HEM 0 WAT 0 SUL 0 
  END 0 DUM 0 Other 6

HTH
Martyn

On Wed, 2011-08-10 at 17:24 +0100, Andreas Förster wrote:
> Dear all,
> 
> how do you extract segments from a pdb file, so that from an input pdb 
> file you get output like this:
> 
> 10-103, 120-174, 200-240
> 
> or, better yet:
> 
> A: 10-103, 120-174, 200-240
> B: 10-104, 120-174, 199-241
> 
> if the N terminus is missing and there are two gaps in the structure.
> 
> I tend to open the pdb file with PyMOL and click on the ends, but a 
> script/command would be much quicker.
> 
> Thanks.
> 
> 
> Andreas
> 
> 

-- 
***
*     *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] low resolution refinement

[Martyn Winn]

Dear All,

An updated ccp4i interface to Refmac 5.6 is available at:

http://www.ccp4.ac.uk/prerelease/refmac5_task_for_ccp4_6.2.tar.gz

You can do "System Administration -> Install/uninstall Tasks" from the
GUI, or just copy the individual files from the tarball to the
$CCP4/ccp4i area. 

This interface includes jelly-body, local NCS and map sharpening. It
will be in the imminent CCP4 6.2.0

HTH
Martyn

On Sat, 2011-07-09 at 12:44 +0200, Robbie Joosten wrote:
> Dear Qixu,
> 
>  
> 
> refamac 5.6 works well at these resolutions. You can add commands to
> your refinement in CCP4i by using the 'Run and view command
> script' (or something like that) option and just typing in the extra
> commands. Jelly-body has worked very well for me (although I use
> tigheter restraints than the default). Also local NCS works well
> (provided you have NCS). I never used reference structures, but I
> heared good things about it. Don't forget to use riding hydrogens, for
> some reason it is not the deafault. 
>  Perhaps you should also switch of the automatic X-ray weighting in
> favour of optimizing the matrix weight yourself (start with 0.05 and
> compare refinements for higher and lower values).
> 
>  
> 
> HTH,
> 
> Robbie
> 
>  
> 
> 
> 
> > Date: Sat, 9 Jul 2011 16:59:29 +0800
> > From: caiq...@gmail.com
> > Subject: [ccp4bb] low resolution refinement
> > To: CCP4BB@JISCMAIL.AC.UK
> >
> > Dear all,
> >
> > Recently, I refine two low resolution structures in refmac 5.5. Their
> > resolutions are 3A and 3.5A respectively.
> > For 3A structure, after MR by phaser and rigidbody refinement&restraint
> > refinement by refmac5.5, I got R factor 25% and R free 35%. And then
> > each time, after my model building in coot and restraint refinement by
> > refmac 5.5, the R factor stays 25%, but R free increases to 38%, even 39%.
> > For 3.5A structure, the R factor stays 27%, but R free increases from
> > 37% to 42% after my slightly model building in coot.
> > Could you help me to find the reason?
> >
> > Maybe the reason is the overfit of the structure? I found that new
> > version of refmac 5.6 has many new features for low resolution
> > refinement, such as jelly boy, secondary structure restraints. But I
> > don't know how to use these new features in old version ccp4i (6.1.13)?
> >
> > I also used phenix.refine with the "reference model" ( I have high
> > resolution model for one domain of the low resolution protein) and
> > "secondary structure restraints", but it seams the same. Any suggestion?
> >
> > BTW, is that simulator annealing not suitable for low resolution
> > structure? I used the simulator annealing method of CNS and
> > phenix.refine, but the geometry of the structure is always destroyed
> > seriously.
> >
> > Could you help me?
> >
> > Thank you very much!  

-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] generate large symmetry model

[martyn . winn]

As well as pdbset, you can use pdbcur. A combination of keywords genunit, symop 
and symcommit.
I’d probably use genunit (applicable to whatever spacegroup you have), followed 
by a second call using symop/symcommit to apply unit cell translations.

Cheers
Martyn

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Hargreaves, David
Sent: 30 June 2011 13:52
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] generate large symmetry model

Does anyone have a rigorous method (or script) for generating an extended 
lattice e.g 3x3x3 unit cells from any pdb file?
Any help gratefully received,

Dave

David Hargreaves
Associate Principal Scientist
_
AstraZeneca
DECS, CP&SS
Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF
Tel +44 (0)01625 518521  Fax +44 (0) 1625 232693
David.Hargreaves @astrazeneca.com

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Re: [ccp4bb] Phaser_EP

[martyn . winn]

Can you post details of versions. Version of CCP4. Version of Phaser (look at 
top of log file).
At one point, the interface was lagging behind the program, but should be ok 
now.

Martyn

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ylva 
Lindqvist
Sent: 28 May 2011 13:31
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Phaser_EP

After updating CCP4 includin Phaser_EP I can not run it - it can not read my 
SIGFs - what is wrong? The error message is " SYNTAX ERROR: Use SIGFPOS SIGF(+) 
or SIG+ " but my mtz-labels are LABIN F+ = F_Fe1(+) SIGF+ = SIGF_Fe1(+) F- = 
F_Fe1(-) SIGF- = SIGF_Fe1(-). I have changed them with SFTOOLS but that did not 
help - always the same error message.

Ylva Lindqvist

Dept. of Medical Biochemistry & Biophysics
Div. of Molecular Structural Biology
KAROLINSKA INSTITUTET
Tomtebodavägen 6
S-171 77 Stockholm, Sweden

Re: [ccp4bb] MrBUMP, P43212 and P41212

[martyn . winn]

I thought so too  It seems to me that there is a typo in the spacegroup 
name in the code. I'll send you some fixed files offline.

Ronan is the expert on queueing systems, but I though the keyword "CLUSTER" 
should be enough. It is supposed to work with SGE. There also seems to be an 
undocumented "QTYPE SGE" keyword. But I can't be sure without trying it.

Cheers
Martyn

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Miguel Ortiz Lombardía
> Sent: 13 May 2011 16:38
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] MrBUMP, P43212 and P41212
> 
> Dear all,
> 
> I get this unexpected (by me) message from MrBUMP:
> 
> Reindex Warning: spacegroup P43212 does not have an enantiomorph
> 
> I thought P41212 and P43212 were enantiomorphs...
> So, am I wrong ?
> 
> (PS: I'm looking for indications on how to use MrBUMP on a cluster with
> a SGE queueing system. Any pointers?)
> 
> Thank you!
> 
> 
> --
> Miguel
> 
> Architecture et Fonction des Macromolécules Biologiques (UMR6098)
> CNRS, Universités d'Aix-Marseille I & II
> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
> Tel: +33(0) 491 82 55 93
> Fax: +33(0) 491 26 67 20
> mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
> http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
> 
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.

Re: [ccp4bb] Script / program to change chain ID 's in symmetry mates

[Martyn Winn]

I wrote a little utility called pdb_merge that is in CCP4. With the
"nomerge" option, it checks for duplicate chain IDs, and renames chains
if necessary.

The main limitation is that it can only merge 2 files, but you should be
able to script a loop to call it multiple times.

What happens if you have 10 chains in the asu and a cubic spacegroup, I
am not sure ...

HTH
Martyn

On Fri, 2011-04-08 at 16:47 +0530, krishan wrote:
> Dear CCP4BB members,
> We are using a script written in python to generate symmetry mates
> for a given pdb file using PYMOL. After generating symmetry mates we
> want to combine all the symmetry molecules in a single PDB file with
> all the chains having unique chain IDs. Since all the symmetry mates
> have same chain ID's  I was wondering if some one knows a script that
> can give unique chain ID for each symmetry mate. We are interested in
> script because that dataset that we are handling is large.
>  I thank you all in advance for your help.
> Best,
> 
> Krishan

-- 
***
*     *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] MR with MD trajectories

[martyn . winn]

I agree there are probably much better and simpler ways of doing this.

But to answer the question, you could probably use MrBUMP to do this, using the 
local PDB file option. It will require a bit of scripting to deal with all the 
file names, and will take forever.

Other points:
1) you don't need to take every frame of the simulation
2) you probably need to minimise each frame
3) you could do clustering to get fewer diverse structures
4) you could do PCA, and use the lowest modes to distort the structure, a la 
normal mode methods

But Poul's approach is still better ...
Martyn

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Poul Nissen 
[p...@mb.au.dk]
Sent: 30 March 2011 07:10
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] MR with MD trajectories

Dear Wandu,

It might be smeared density because it is missing from your phasing model, so 
no reason to reinvent the wheel with MD and Phaser. You see electron density 
features for the domain and you know its basic structure. You can place the 
domain manually - it would take you five minutes and then you can proceed to 
refine the position by rigid body refinement and ordinary refinement/rebuilding

Poul


On 30/03/2011, at 05.43, Vandu Murugan wrote:

> Dear all,
> I have a protein molecule with two flexible domains.  For a 2.8 angstrom 
> data, I could get  MR solution for the larger domain but not for the smaller 
> domain (around 80 aminoacids).  The second domain appears as extra density 
> showing its presence , but does not allow manual model building on it, since 
> it appers to be smeared.  I would like to run a phaser  with some 3 
> structures that I have for this protein from a simulation.  Would it be 
> possible to do this in my computer?  If so, how can I do this?  Any 
> suggestions on this will be appreciated.  Thanks in advance.
>
> regards,
> Wandu
>
>

Re: [ccp4bb] Data file wrangling question

[martyn . winn]

oops, I did that ... and I'd forgotten all about it ... simpler option than 
pointless
m

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> James Holton
> Sent: 18 March 2011 15:49
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Data file wrangling question
> 
> REBATCH
> 
> 
> On 3/18/2011 2:43 AM, Graeme Winter wrote:
> > Hi Folks,
> >
> > Before I try to write a new program, I thought I would check what I
> > want to do can't be done
> >
> > I have many unmerged but scaled & summed MTZ files from scala (output
> > unmerged) for which I would like to simply change the DNAME. I tried
> > CAD, but it complains about the multi-record nature of the files and
> > discusses unmitigated disasters, which can't be a good thiing. More
> > helpfully it suggests use MTZUTILS instead.
> >
> > MTZUTILS can't change the DNAME according to the documentation.
> >
> > Any suggestions? I can clearly write a little jiffy program to do
> this
> > but it seems like a simple thing someone would want to do.
> >
> > Thanks,
> >
> > Graeme

Re: [ccp4bb] Data file wrangling question

[Martyn Winn]

How about pointless? It seems to have a NAME keyword that does what you
want? Caveat: I have never tried this myself. You may have to do an
identity reindexing or similar.

You are right in your assessment of CAD and MTZUTILS. In principle, the
functionality should be in mtzutils, but I doubt that it would be easy
to add.

m

On Fri, 2011-03-18 at 09:43 +, Graeme Winter wrote:
> Hi Folks,
> 
> 
> Before I try to write a new program, I thought I would check what I
> want to do can't be done
> 
> 
> I have many unmerged but scaled & summed MTZ files from scala (output
> unmerged) for which I would like to simply change the DNAME. I tried
> CAD, but it complains about the multi-record nature of the files and
> discusses unmitigated disasters, which can't be a good thiing. More
> helpfully it suggests use MTZUTILS instead.
> 
> 
> MTZUTILS can't change the DNAME according to the documentation.
> 
> 
> Any suggestions? I can clearly write a little jiffy program to do this
> but it seems like a simple thing someone would want to do.
> 
> 
> Thanks,
> 
> 
> Graeme

-- 
***
*     *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] TLS from PDB records

[martyn . winn]

tlsextract in the CCP4 suite (from Jay Painter and Ethan Merritt).

Martyn

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jochen 
Kuper
Sent: 03 February 2011 08:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] TLS from PDB records

Dear All,


sorry for the probably silly question but the matter is somewhat urgent and I 
cant seem to find an appropriate solution ...


I need to pull out the TLS params for a deposited pdb with partial B and use 
those parameters to calculate the total B factor. My problem is that I cant 
find a program that reads those params and puts them in a format TLSANL can 
read.

I am probably missing something obvious here 


Many thanks in advance.


Cheers,

Jochen


-
Dr. Jochen Kuper
Rudolf Virchow Center for Biomedical Research
Josef Schneider Strasse 2, Haus D15
97070 Wuerzburg
+49 (0) 9313180391
jochen.ku...@virchow.uni-wuerzburg.de

Re: [ccp4bb] Saxs reviews or books

[Martyn Winn]

Polite etiquette reminder:
1. Large attachments are discouraged
2. Articles are usually covered by copyright
See http://www.ccp4.ac.uk/ccp4bb.php

Cheers
Martyn

On Tue, 2011-01-11 at 07:31 +0100, Catarina Rodrigues wrote:
> Hi,
> 
> 
> I recommend you the reviews attached, which have help me a lot.
> 
> 
> Regards
> 
> 
> Catarina
> 
> 
> 
> 
> -- 
> This message has been scanned for viruses and 
> dangerous content by MailScanner, and is 
> believed to be clean. 
> 
> 
> -- 
> Catarina Rodrigues, PhD Student
> Molecular Transport & Signalling
> AFMB UMR 6098 CNRS/UI/UII Case 932 
> 163 Avenue de Luminy 
> 13288 Marseille cedex 9 (France) 
> Tel : +33 04 91 82 55 60
> Fax : 04 91 26 67 20
> e-mail:catarina.rodrig...@afmb.univ-mrs.fr
> http://www.afmb.univ-mrs.fr/
> 
> 
> 
> 
> 
> 
> Le 11 janv. 2011 à 01:33, Rojan Shrestha a écrit :
> 
> > Hello:
> >  
> > I am very novice about Small Angle X-ray Scattering. I am looking
> > for introductory books or review papers. Could you recommend this
> > type of document?
> >  
> > Regards,
> >  
> > Rojan
> > 
> > -- 
> > This message has been scanned for viruses and 
> > dangerous content by MailScanner, and is 
> > believed to be clean.
> 

-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

[ccp4bb] Job posting: EM Software Developer

[martyn . winn]

Forwarded on behalf of Alan Roseman [mailto:alan.rose...@manchester.ac.uk] so 
please contact him not me.

Happy New Year to all,

Martyn



Software Developer/ Scientific Computer Programmer
We are looking for a Software Developer or Scientific Computer Programmer to 
develop   

interesting new software applications for Electron Microscopy. 

Follow the link below for more details:





http://www.manchester.ac.uk/aboutus/jobs/vacancies/research/vacancy/index.htm?ref=177549







I'd appreciate it if you would bring it to the attention of anyone who may be 
interested.







==



Faculty of Life Sciences, University of Manchester, UK.



Closing date:8/1/2011 - Reference: LS/10769



The post is funded by the BBSRC, for up to 15 months.



Salary £24,273 - £27,319 p.a.



Informal enquiries



Dr Alan Roseman

Tel: + 44 (0) 161 275 7226

Email alan.roseman at manchester.ac.uk 
 





http://www.manchester.ac.uk/aboutus/jobs/vacancies/research/vacancy/index.htm?ref=177549











 

Re: [ccp4bb] limit for number of files for CAD...

[Martyn Winn]

Yes, CAD is limited to 9 input files. I seem to remember I once tried to
increase the limit, but got into problems (it is not just a case of
increasing MAXFILES). It is far simpler and safer to run CAD
iteratively.

But an MTZ file can hold more. The current limits are:
#define MXTALS  100  
#define MSETS  1000 
#define MCOLUMNS  1 

In principle, we could remove these limits, but I guess they are ok in
most normal cases ...

m


On Wed, 2010-11-03 at 18:20 +0100, Rita GIORDANO wrote:
> Hello,
> 9 mtz files are the limit of CAD, one things you can do is to modify the 
> source file , that is wrote in fortran, or write a bash script or  that 
> run iteratively the CAD script and change the MTZ files.
> 
> R.
> 
> On 03/11/2010 18:11, Francis E Reyes wrote:
> > CCP4'ers,
> >
> > Are 9 datasets the maximum for an mtz file? or a single run of cad? The
> > manual (http://www.ccp4.ac.uk/html/cad.html) seems to suggest that 9 is
> > the limit per cad run but not for a given mtz.
> >
> > F
> >
> >
> >
> > -
> > Francis E. Reyes M.Sc.
> > 215 UCB
> > University of Colorado at Boulder
> >
> > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
> >
> > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
> 

-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] Bug in c_truncate?

[Martyn Winn]

The GUI task has the option to run (c)truncate after f2mtz (if you have
intensities in the input hkl file), and then uniqueify after that.

I can reproduce this problem. ctruncate is losing the freeR column. At
the moment, I don't know if this is a bug or a feature.

As a work around, you can run ctruncate for the analyses, and re-run
with truncate for the MTZ file.

Tim is right, you need to use 0 instead of -1 in the CCP4 convention.

HTH
Martyn

PS Refmac is moving towards using intensities, so that you can avoid
this step. But I believe 5.5 only uses intensities for twin refinement.

On Thu, 2010-10-28 at 17:55 +0100, Phil Evans wrote:
> Why are you running [c]truncate? this is used to convert I -> F and I would 
> be surprised if it recognised or preserved a FreeR column
> 
> Phil
> 
> On 28 Oct 2010, at 17:48, Peter Chan wrote:
> 
> > Hello Tim,
> > 
> > Thank you for the suggestion. I have now tagged the working set as "1" and 
> > test set as "0". Unfortunately, it still gives the same error about all 
> > Rfree being the same, and only in c-truncate but not old-truncate. Perhaps 
> > I should install 6.1.3 and see if the problem still persist.
> > 
> > Best,
> > Peter
> > 
> > > Date: Thu, 28 Oct 2010 16:29:31 +0200
> > > From: t...@shelx.uni-ac.gwdg.de
> > > Subject: Re: [ccp4bb] Bug in c_truncate?
> > > To: CCP4BB@JISCMAIL.AC.UK
> > > 
> > > Hello Peter,
> > > 
> > > I faintly rememeber a similar kind of problem, and think that if you 
> > > replace
> > > "-1" with "0", the problem should go away. It seemed that "-1" is not an 
> > > allowed
> > > flag for (some) ccp4 programs.
> > > 
> > > Please let us know if this resolves the issue.
> > > 
> > > Tim
> > > 
> > > On Thu, Oct 28, 2010 at 10:21:20AM -0400, Peter Chan wrote:
> > > > 
> > > > 
> > > > 
> > > > 
> > > > Dear Crystallographers,
> > > > 
> > > > Thank you all for the emails. Below are some details of the procedures 
> > > > I performed leading up to the problem.
> > > > 
> > > > The reflection file is my own data, processed in XDS and then flagging 
> > > > FreeR's in XPREP in thin resolution shells. I am using CCP4i version 
> > > > 6.1.2. I tried looking for known/resolved issues/updates in version 
> > > > 6.1.3 but could not find any so I assumed it is the same version of 
> > > > f2mtz/ctruncate/uniqueify.
> > > > 
> > > > 
> > > > I used the GUI version of F2MTZ, with the settings below:
> > > > 
> > > > - import file in SHELX format
> > > > 
> > > > - "keep existing FreeR flags"
> > > > 
> > > > - fortran format (3F4.0,2F8.3,F4.0)
> > > > 
> > > > - added data label "I other integer" // FreeRflag
> > > > 
> > > > The hkl file, in SHELX format, output by XPREP look something like this:
> > > > 
> > > > -26 -3 1 777.48 39.19
> > > > 26 -3 -1 800.83 36.31
> > > > -26 3 -1 782.67 37.97
> > > > 27 -3 1 45.722 25.711 -1
> > > > -27 3 1 -14.20 31.69 -1
> > > > 
> > > > Notice the test set is flagged "-1" and the working set is not flagged 
> > > > at all. This actually lead to another error message in f2mtz about 
> > > > missing FreeR flags. From my understanding, the SHELX flagging 
> > > > convention is "1" for working and "-1" for test. So I manually tagged 
> > > > the working set with "1" using vi:
> > > > 
> > > > -26 -3 1 777.48 39.19 1
> > > > 26 -3 -1 800.83 36.31 1
> > > > -26 3 -1 782.67 37.97 1
> > > > 27 -3 1 45.722 25.711 -1
> > > > -27 3 1 -14.20 31.69 -1
> > > > 
> > > > This is the file which gives me the error message: "Problem with FREE 
> > > > column in input file. All flags apparently identical. Check input 
> > > > file.". Apparently, import to mtz works ok when I use old-truncate 
> > > > instead of c-truncate.
> > > > 
> > > > Best,
> > > > Peter
> > > > 
> > > -- 
> > > --
> > > Tim Gruene
> > > Institut fuer anorganische Chemie
> > > Tammannstr. 4
> > > D-37077 Goettingen
> > > 
> > > phone: +49 (0)551 39 22149
> > > 
> > > GPG Key ID = A46BEE1A
> > > 

-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] protein ligand energy

[Martyn Winn]

This is all true. And I think the bottom line is that it is extremely
non-trivial to get a meaningful number.

The Amber MM-PBSA script is the best established one. We have an
equivalent CHARMM-based script at:
http://www.cse.scitech.ac.uk/cbg/software/charmm/

But I guess this is beyond the original question. A simpler option (but
more approximate) would be to run the PDB of the modelled complex
through PISA (online or CCP4 version) and look at the results for the
protein ligand interface.

Cheers
Martyn

On Wed, 2010-10-13 at 15:15 +0100, Robert Esnouf wrote:
> Dear Rex,
> 
> It certainly matters what you mean by the "energy" of a 
> protein ligand complex. And whether you are comparing a series 
> of related similar structures or looking for an "absolute" 
> energy.
> 
> The problem is that there is no such thing as an "absolute" 
> energy, it is always relative to something else. Typically, 
> you might calculate the the binding free energy (delta G) for 
> the components in aqueous solution. If you were looking at the 
> (small) differences between related structures then you'd look 
> at the change (delta delta G) and hope the other errors 
> largely cancel out.
> 
> One method for which there is substantial literature is based 
> on Amber simulations. There are even sample scripts to do the 
> correct job. You simulate the complex in a water box and 
> sample the conformation every so many steps. You then discard 
> the waters and use something like the Poisson-Boltmann method 
> to estimate solvation free energies for the complex and the 
> isolated components. The difference is then your estimation of 
> the binding free energy.
> 
> In all such simulations it is the effect of the solvent 
> (partial charges, dielectric properties and entropic effects) 
> that are likely to dominate the calculation. You have to do 
> your best to include them as realistically as possible.
> 
> Amber is not free, but not expensive and your institution 
> probably already has a site licence. Other simulation programs 
> would also do the job (probably just as well!) but I am not 
> aware they have available scripts.
> 
> 
> Best wishes,
> Robert
> 
> --
> 
> Dr. Robert Esnouf,
> University Research Lecturer
> and Head of Research Computing,
> Wellcome Trust Centre for Human Genetics,
> Roosevelt Drive, Oxford OX3 7BN, UK
> 
> Emails: rob...@strubi.ox.ac.uk   Tel: (+44) - 1865 - 287783
> and rob...@esnouf.comFax: (+44) - 1865 - 287547

-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

[ccp4bb] Job for scientific programmer, for Electron microscopy applications

[Martyn Winn]

Enquiries to Alan Roseman, please.
m

> Scientific Programmer, for Electron microscopy applications:
> Faculty of Life Sciences, University of Manchester, UK
> 
> Closing date: 14/09/2010, Reference: LS/10769
> 
> We seek a scientific programmer with an interest in structural biology  
> to join Dr Alan Roseman's group. Single particle analysis using  
> electron microscopy is a powerful and versatile technique for  
> determining molecular structures, and near atomic resolutions have  
> been be reached with some specimens. We are pioneering new methods for  
> analysis of structures of macromolecular complexes using electron  
> cryo-microscopy, making use of novel correlation functions and network  
> analysis.
> 
> You will develop and program new software applications and algorithms,  
> and field test these on laboratory projects. Expertise in high  
> performance computing, and programming in the Fortran 90 and python  
> languages is required.
> 
> You will have degree in computer science, computational biology,  
> engineering, or a related field (or equivalent experience).
> 
> The post is funded by the BBSRC, starting from 1 November 2010 for up  
> to 15 months.
> Salary
> 
> £24,273 - £27,319 p.a.
> Informal enquiries
> 
> Dr Alan Roseman
> Tel: + 44 (0) 161 275 7226
> Email alan.rose...@manchester.ac.uk

-- 
*******
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] Fd-3m with pdbset

[Martyn Winn]

> > There seem to be a few CCP4 Fortran files that have character spgnam*10
> > from the good old days ...
> 
> What good old days were those? The Cryst1-format for PDB-files in the ccp4
> documentation says
> 56-66Space group symbol, left justified (not used)
> which is eleven characters. Were there days when this was different?
> 
> Tim

I remember when we didn't bother with spacegroup on the
CRYST1 line at all, let alone formatting it correctly.

And what about 'P 42/n n m :2' which is more than 11 characters?

I realise my answer doesn't help with Coot problems, but I will clean up
CCP4 Fortran programs at least.

m

-- 
***
*     *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] Fd-3m with pdbset

[Martyn Winn]

Yes, I can reproduce this, and I think I have found the bug.
It is simply that PDBSET dimensions the spacegroup name to 10
characters. Increasing that to 20 allows you to use either

spac 'F d -3 m :1'
or
spac 227

However, it still won't recognise 'F d -3 m' because this is not in the
syminfo file (at least, not in a field that is read).

There seem to be a few CCP4 Fortran files that have character spgnam*10
from the good old days ...

Cheers
Martyn

On Mon, 2010-09-06 at 13:38 +0200, Tim Gruene wrote:
> Hello,
> I tried to assign a cell with space group F d -3 m to a PDB file using pdbset.
> Since it did not recognize the string 'F d -3 m' (nor 'F d -3 m :1') , I used
> the space group number 227. This resulted in the space group string 'F d -3 m 
> :'
> in the PDB-file instead of 'F d -3 m :1' as it is listed in syminfo.lib, and
> hence coot refused to display the symmetry mates for the molecule.
> 
> When I add the missing '1' in the resulting PDB-file, coot does display the
> cell, but when I ask to display the symmetry mates, coot chokes and consumed 
> all
> my cpu power (for 8 molecules present in the unit cell...) until I killed it.
> 
> I was wondering if this is a known bug in syminfo.lib (and/or the dependent
> programs) and if there is a way around it (without using
> phenix.get_me_out_of_here, I could of course use xp instead of coot for such a
> small molecule).
> 
> Kind regards, Tim
> 
> P.S.: The bug in pdbset persits also in pdbset from ccp4-6.1.3
> 

-- 
*******
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC

[Martyn Winn]

Hi,

Yes, zero origin is a sure sign that it hasn't identified the atoms in
the TLS group.

There is presumably some problem matching atom names, but am not sure
what. If you send me the files, I can have a play.

However, you might have problems with the group definitions anyway. I
seem to remember that TLS is not stable for 3 atoms. In any case, you
have more TLS parameters (20) than anisotropic parameters (3*6). 

It does sound like that's what they did in the Nat. Struct. Biol. but
they seem to have deposited the pre-TLS coordinates from CNS, so hard to
tell.

Cheers
Martyn


On Thu, 2010-07-15 at 15:54 +0100, Huw Jenkins wrote:
> Hi,
> 
> I am currently refining some reasonably high (1.4-1.6 Å) resolution
> protein:RNA complex structures and was trying the approach described
> in Schwartz et al. Nat. Struct. Biol. 8 (2001) 761-765 where they
> divided each nucleotide into three TLS groups  – the ribose, the
> phosphorus atom plus both nonesterified oxygens and the base. 
> 
> When I define a tlsin file that does this with the ribose, P OP1 and
> OP2, and base from 3 successive nucleotides everything seems to work
> fine so the groups are defined correctly. However when I divide a
> single nucleotide into 3 TLS groups only the first group has its
> origin calculated and actually has TLS parameters refined:
> 
> 
> TLS origin for group1  -3.1622999  -6.9280601  -9.6330261 
>
> TLS origin for group2   0.000   0.000   0.000 
>
> TLS origin for group3   0.000   0.000   0.000 
>   
> 
> TLS group1:   
>   
>  T tensor ( 1) =0.046   0.115   0.103  -0.003  -0.008   0.087
>  L tensor ( 1) =1.341   1.887   5.684   0.509  -2.040  -0.436
>  S tensor ( 1) =0.015   0.015  -0.257  -0.220  -0.024   0.071   0.095   
> 0.060
> 
> TLS group2:   
>   
>  T tensor ( 2) =0.031   0.031   0.031   0.000   0.000   0.000
>  L tensor ( 2) =0.000   0.000   0.000   0.000   0.000   0.000
>  S tensor ( 2) =0.000   0.000   0.000   0.000   0.000   0.000   0.000   
> 0.000
> 
> TLS group3:   
>   
>  T tensor ( 3) =0.031   0.031   0.031   0.000   0.000   0.000
>  L tensor ( 3) =0.000   0.000   0.000   0.000   0.000   0.000
>  S tensor ( 3) =0.000   0.000   0.000   0.000   0.000   0.000   0.000   
> 0.000
> 
> 
> An excerpt from my tlsin is below:
> 
> TLS
> RANGE  'B   3.' 'B   3.' P
> RANGE  'B   3.' 'B   3.' O1P
> RANGE  'B   3.' 'B   3.' O2P
> 
> TLS
> RANGE  'B   3.' 'B   3.' C1*
> RANGE  'B   3.' 'B   3.' C2*
> RANGE  'B   3.' 'B   3.' C3*
> RANGE  'B   3.' 'B   3.' C4*
> RANGE  'B   3.' 'B   3.' C5*
> RANGE  'B   3.' 'B   3.' O2*
> RANGE  'B   3.' 'B   3.' O3*
> RANGE  'B   3.' 'B   3.' O4*
> 
> 
> TLS
> RANGE  'B   3.' 'B   3.' N1
> RANGE  'B   3.' 'B   3.' C2
> RANGE  'B   3.' 'B   3.' O2
> RANGE  'B   3.' 'B   3.' N3
> RANGE  'B   3.' 'B   3.' C4
> RANGE  'B   3.' 'B   3.' O4
> RANGE  'B   3.' 'B   3.' C5
> RANGE  'B   3.' 'B   3.' C6
> 
> I guess I've got the syntax of the tlsin file wrong? Any suggestions for 
> what's wrong would be much appreciated!
> 
> Thanks,
> 
> 
> Huw 
> 
> 
> 
> --
> Dr Huw Jenkins
> Astbury Centre for Structural Molecular Biology 
> University of Leeds
-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
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***

Re: [ccp4bb] conversion of cyroEM reconstruction from MRC to CCP4 format

[Martyn Winn]

Which is why I said "make available" rather than "post it" or "email
me" :)

And he has done just that  will go have a look 

m

On Tue, 2010-07-13 at 18:42 -0700, James Holton wrote:
> 
> The original poster just told me that the map file is 2.6 GB.  Please
> don't encourage him to attach it to a ccp4bb email!
> 
> -James Holton
> MAD Scientist
> 
> 
> On Tue, Jul 13, 2010 at 2:58 PM,  wrote:
> Actually, zero spacegroup should be tolerated by the CCP4
> library now.
> 
> We were recently alerted to another problem, caused by
> non-zero origin in the EM map header. But I think this is
> different to the problem of the original poster.
> 
> It's probably fair to say we haven't tested enough against
> real EM maps, and perhaps we should.
> 
> Perhaps the original poster could make their problem maps
> available??
> 
> Cheers
> Martyn
> 
> 
> -Original Message-
> From: CCP4 bulletin board on behalf of Christoph Best
> Sent: Tue 7/13/2010 10:20 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] conversion of cyroEM reconstruction from
> MRC to CCP4 format
> 
> Hello,
> 
> we have found that there are some minor issues in MRC files
> using in Em
> that can make them unpalatable to the CCP4 map library. You
> can easily
> look at header fields in Python - here is a sample program to
> quickly
> check some of the more common problems.
> 
>from struct import *
> 
>header=file('your_file_name.map').read(1024)
>print 'dimensions=',unpack_from('iii',header,0)
>print 'mode=',unpack_from('i',header,3*4)[0],'should be 0,
> 1, or 2'
>print 'space
> group=',unpack_from('i',header,22*4)[0],'should be 1'
>print 'magic=',unpack_from('',header,52*4),'should be
> (\'M\', \'A\', \'P\', \' \')'
>print 'machine stamp=','%x' %
> unpack_from('i',header,53*4),' should be 4144 or '
>print 'nsymbt=',unpack_from('i',header,23*4)[0],' should be
> 0'
> 
> The issues we typically encountered were bad space groups
> (zero), wrong
> machine stamps (they should be 0x or 0x4144), missing the
> "magic
> bytes" that spell "MAP ", or a value of nsymbt that indicates
> the
> presence of additional symmetry information following the
> header, which
> is then missing.
> 
> Chimera ignores most of these issues.
> 
> -Christoph
> 
> --
> | Christoph Best 
> http://www.ebi.ac.uk/~best
> | European Bioinformatics Institute, Cambridge, UK
> +44-1223-492649
> 
> 
-- 
***
* *
*   Dr. Martyn Winn   *
* *
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***

Re: [ccp4bb] conversion of cyroEM reconstruction from MRC to CCP4 format

[martyn . winn]

Actually, zero spacegroup should be tolerated by the CCP4 library now.

We were recently alerted to another problem, caused by non-zero origin in the 
EM map header. But I think this is different to the problem of the original 
poster.

It's probably fair to say we haven't tested enough against real EM maps, and 
perhaps we should. 

Perhaps the original poster could make their problem maps available??

Cheers
Martyn

-Original Message-
From: CCP4 bulletin board on behalf of Christoph Best
Sent: Tue 7/13/2010 10:20 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] conversion of cyroEM reconstruction from MRC to CCP4 
format
 
Hello,

we have found that there are some minor issues in MRC files using in Em
that can make them unpalatable to the CCP4 map library. You can easily
look at header fields in Python - here is a sample program to quickly
check some of the more common problems.

from struct import *

header=file('your_file_name.map').read(1024)
print 'dimensions=',unpack_from('iii',header,0)
print 'mode=',unpack_from('i',header,3*4)[0],'should be 0, 1, or 2'
print 'space group=',unpack_from('i',header,22*4)[0],'should be 1'
print 'magic=',unpack_from('',header,52*4),'should be (\'M\', \'A\', 
\'P\', \' \')'
print 'machine stamp=','%x' % unpack_from('i',header,53*4),' should be 4144 
or '
print 'nsymbt=',unpack_from('i',header,23*4)[0],' should be 0'

The issues we typically encountered were bad space groups (zero), wrong
machine stamps (they should be 0x or 0x4144), missing the "magic
bytes" that spell "MAP ", or a value of nsymbt that indicates the
presence of additional symmetry information following the header, which
is then missing.

Chimera ignores most of these issues. 

-Christoph

-- 
| Christoph Besthttp://www.ebi.ac.uk/~best
| European Bioinformatics Institute, Cambridge, UK +44-1223-492649

Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot

[Martyn Winn]

You should be able to use the CCP4 utility "coord_format" though this is
not in the GUI:

coord_format xyzin ./1ivo.cif xyzout 1ivo.pdb < Dear All,
>  
> I am looking for a ccp4 program that reads in cif-files and converts
> them into pdb-files, including the CRYST1 card. Can anybody suggest a
> solution? I didn't find any in ccp4i, e.g. the coordinate utilities.
>  
> I also tried COOT to read in cif-files (downloaded from the pdb
> server). For one example it crashed, for others it doesn't colour the
> bonds properly if "Bonds (Colour by Atom)"  is chosen but shows
> all bonds in one colour. Is that a known feature? If I save these
> coordinates in pdb-format and try to read it back, I get an ERROR
> saying: "Wrong ASCII format of an integer". 
>  
>  
> Thanks for any suggestions
> Christian Engel
> 
> 
>  
> Mit freundlichen Grüßen / Best regards / Cordialement 
> 
> Dr. Christian Engel 
> 
> Sanofi-Aventis Deutschland GmbH
> R&D CAS Structural Biology FFM
> Industriepark Hoechst
> Bldg. G877, Room 020
> D-65926 Frankfurt am Main
> t: +49 69 305 12946
> f: +49 69 305 80169
> w:www.sanofi-aventis.de 
> 
> 125 Jahre Arzneimittel aus Deutschland von sanofi-aventis
> 
> 
> *
> Sanofi-Aventis Deutschland GmbH ·  Sitz der Gesellschaft:
> Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B
> Nr. 40661
> Vorsitzender des Aufsichtsrats: Hanspeter Spek -
> Geschäftsführer: Dr. Martin Siewert (Vorsitzender), Ulf
> Bialojahn, Dr. Matthias Braun,
> Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken,
> Dr. Heinz Riederer
> 
> *
> 
> 
-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
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***

Re: [ccp4bb] How to calculate real-space CC by section?

[Martyn Winn]

You might find some useful examples in $CCP4/examples/unix/runnable
OVERLAPMAP is used in mapcorrelation_procedures, overlapmap.exam,
waterpeaks.

As I understand it, CORR SECT does a map correlation by map section, so
you get a single CC value per map section.
This mode does not use MAPIN3, and doesn't use atom or residue
information. So yes, it will ignore the CHAIN keyword.

"section" refers to map section:

  Number of columns, rows, sections ...   96  152   17

and not a section of your atomic model.

HTH
Martyn



On Tue, 2010-05-25 at 23:51 -0400, Hailiang Zhang wrote:
> Hi,
> 
> I am working on a real space correlation on a specif protein section using
> CCP4 OVERLAPMAP. I am using the following scripts, not sure whether it is
> good or not (didn't find in OVERLAPMAP documentation).
> 
> overlapmap   \
>mapin1 ${PDB}-1.map\
>mapin2 ${PDB}-2.map\
>mapin3 ${PDB}-mask.map \
> < CORR SECT
> CHAIN A $START $END
> END
> 
> There is no error message, but the results make no difference no matter
> how I change $START and $END. I am not sure whether the above script is
> ok.
> 
> By the way, more importantly to me, if corr sect works at all, will it
> print out a single CC value by integrating over the WHOLE region define by
> the section range?
> 
> Thanks!
> 
> Best Regards, Hailiang
-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
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***

Re: [ccp4bb] TLSANL total B factor question

[Martyn Winn]

That was a bug in TLSANL, introduced in 6.1.0 and fixed in 6.1.2. 
So you need to update your CCP4, or at least extract a newer tlsanl
binary. Apologies for that.

Martyn

On Fri, 2010-05-21 at 04:46 +0100, Shiva Kumar wrote:
> Dear Crystallographers
> 
> I am trying to  print out my total B factors using TLSANL (version: 6.1) in 
> CCP4- 6.1.1.   My TLSANL’s input file.pdb is coming from refmac (version: 
> 5.5.0072) using the TLS & restraint refinement option and isotropic B 
> factors. The TLSANL’s output file.pdb contains the following ATOM and ANISOU 
> records as an example.
> 
> REMARK   3  TLS DETAILS
> REMARK   3   NUMBER OF TLS GROUPS  :2
> REMARK   3   ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
> REMARK   3   ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
> 
> ATOM 88  C   ASN A  14   0.748  -5.841  -6.258  1.00 35.84   C
> ANISOU   88  C   ASN A  14 5335   4549   3734  0  0  0   C
> ATOM 89  O   ASN A  14   0.807  -6.941  -6.845  1.00 35.04   O
> ANISOU   89  O   ASN A  14 5229   4375   3709  0  0  0   O
> 
> 
> I am not able to understand why my ANISOU record contains ‘0 0 0’ for the 
> anisotropic component.  Something is not correct and I'm not sure why I am 
> not able to print out my total B factors.
> 
> I would appreciate it if someone could tell me what is going wrong and how 
> can I print my total B factors.
> 
> 
> Thanks
> Regards
> Shiva Kumar
-- 
***
*     *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
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***

Re: [ccp4bb] automise ncont

[Martyn Winn]

See $CCP4/examples/unix/runnable/ncont.exam

Run as e.g. ncont.exam > ncont.log

Cheers
Martyn

On Thu, 2010-04-29 at 06:42 -0700, Thomas Juettemann wrote:
> Dear all,
> 
> I am pretty new to the CCP4 suite. I am trying to automise the
> execution and parsing of ncont.
> Could someone advise me how (if possible) to pass parameters to the program?
> 
> I am trying to do something like
> 
> bin/ncont XYZIN 1FNT_BJ.pdb
> source /*/B
> target /*/J
> maxdist 6.0
> 
> and have the output redirected into a file.
> 
> Thank you for your time!
> 
> Best wishes,
> Thomas
-- 
***
*         *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
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***

Re: [ccp4bb] _diffrn.detail in PDB sf.cif releases

[Martyn Winn]

I'll update the CCP4 version of the dictionary
(ccp4/lib/data/cif_mm.dic). Thanks for the heads-up.

As you say, the workaround meanwhile is to edit the .cif file to
remove/change any offending lines. 

Martyn

On Wed, 2010-03-03 at 11:24 +, Thomas Womack wrote:
> I notice that a fair number of PDB-deposited sets of structure factors
> in sf.cif format (fourteen of them in the March 2 2010 release)
> contain an _diffrn.detail line; this comes to my attention because
> ccp4-6.1.2's cif2mtz falls over when it encounters such a line and I
> have to edit the CIF manually to get it to continue.
> 
> I have never observed this line to have a value other than '?'; is it
> known what software produces sf.cif files with this meaningless and
> problematic line in, and how to make it stop?
> 
> http://mmcif.rcsb.org/dictionaries/mmcif_pdbx.dic/Categories/diffrn.html
> 
> does not mention _diffrn.detail, although it offers an optional
> _diffrn.details line, and one example where that was used to describe
> a data-gathering protocol where exposure increased over time.
> 
> Tom
-- 
***
*     *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
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***

Re: [ccp4bb] verifying a molecular replacement solution (test case where the true structure is known)

[Martyn Winn]

reforigin
http://www.ccp4.ac.uk/dist/html/reforigin.html
Does exactly what you want, but requires that the 2 PDB files have the
same atoms - the CAONLY option can help with missing atoms, but it still
won't work unless you have mutated your search model to the target
sequence.

solution_check
A utility from the Balbes package, included as a stand-alone binary in
the latest ccp4.

Alternative origins are documented in:
http://www.ccp4.ac.uk/dist/html/alternate_origins.html

HTH
Martyn

On Mon, 2010-01-18 at 11:47 +0900, Francois Berenger wrote:
> Hello,
> 
> 1) In the case I know the true structure (I am verifying I use Phaser
> correctly), is there a program to do so?
> 
> Some other questions, if I am to write this program by myself:
> 
> 2) is there a list somewhere of the translation ambiguities for
> each spacegroup?
> For example, in P1 it would say me any translation on any axis
> is fine.
> 
> 3) is there a list of permissible origins for each space group?
> For example, in P212121 it would say me there are 8 possible choices
> and list them for me.
> 
> I already know of symop.lib, but I don't think it has some of the 
> information I am looking for.
> I also know the csymmatch example program of the clipper library, it 
> does part of what I intend to do.
> 
> Thanks a lot,
> Francois.
-- 
***
*     *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
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***

Re: [ccp4bb] H32 or R 3 2 :H

[Martyn Winn]

I have no opinion on what should be written (such debates are a world of
pain) but I tried to make csymlib accept anything.

I tried ncont (as an example of a C++ program) and contact (as an
example of a Fortran program) and both seemed happy with such a CRYST1
line. CCP4 is pretty heterogenous, so I can well believe there may be
exceptions. Could you give me a hint where the problems are?

Cheers
Martyn

On Mon, 2009-12-14 at 17:04 +, Eleanor Dodson wrote:
> hypFdemo_28.pdb:
> CRYST1   58.351   58.351  155.876  90.00  90.00 120.00 R 3 2 :H  1
> 
> I dont hold a candle for either of these SGs but Phaser is now 
> outputting the R 3 2 :H  and many many other CCP4 programs are then 
> falling over
> 
> Can the symlib be modified to accept both?
> Eleanor
-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
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* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] methews coefficient and validation of 60mer

[Martyn Winn]

Yes, matthews_coef has a limit of 48. You need to change:
  PARAMETER (MAXMOL=48)
in $CPROG/matthews_coef.f and recompile. Ask if you need help with
this. 
So looks like its time to increase the parameter in line with the
capabilities of computers and crystallographers 
BTW matthews won't tell you 60, it will tell you somewhere between 40
and 80. Also I assume this is protein - I have fixed the matthews task
recently for RNA/DNA.

The CCP4 Procheck Ramachandran is deprecated, since it is based on old
angle distributions. Try Rampage, e.g. via the ccp4i -> Validation &
Deposition -> Validate Model and/or Data task.

Cheers
Martyn

On Wed, 2009-12-02 at 12:57 +0530, Pankaj Chauhan wrote:
> Hi ,
> In one of my 60mer structure at 3.5 A, , when I run methews in ccp4i,
> it doesn't show number of molecules in asymmetry above 40,  is there
> any other program which can show all the molecules in assymetric unit.
> Second problem, for validation of 60mer, i was willing to use
> Procheck which gives residues in allowed region, additional allowed
> region, generously allowed region and disallowed region in
> ramachandran plot. But procheck is not giving any output here in
> 60mer. Although i could validate the structure using coot and phenix,
> but they dont give residues in generously allowed region. 
> KIndly give some suggestion and help,
> Regards,
> 
> -- 
> Pankaj Chauhan
> Senior Research Fellow, PhD Scholar
> Crystallography Laboratory
> Division of Protein Science & Engg.
> IMTECH , Chandigarh, INDIA
-- 
***
*     *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603825Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] refmac5/ccp4i GUI error

[Martyn Winn]

Mmmm. This rings a bell. It is either:

1) an infelicity re-running an old job - start from a new task window
2) the user has a file ~/.CCP4/CCP4I_TOP/tasks/refmac5.def - delete it

If it is really only "one" of your users, then it is probably the
second ...

HTH
Martyn

On Thu, 2009-11-19 at 13:59 -0500, Ben Eisenbraun wrote:
> Howdy All,
> 
> The refmac5 ccp4i GUI is barfing for one of my users.  The GUI error is:
> 
> can't read "array(NATOMS)": no such element in array
> can't read "array(NATOMS)": no such element in array
> while executing
> "if {$array(N_DEPFRAMES_$def_proc0) >= 0 && $array($indexVar) > 0 } {
> append array(UPDATE_SCRIPTS)  "update_toggleframe $def_proc0 0 $arrayname
> $in..."
> (procedure "CreateToggleFrame" line 98)
> invoked from within
> "CreateToggleFrame NATOMS atom_proc  "Add another atomic form factor"  "Atomic
> form factors"  "Add Atom"  [list  ATOM  ATOM_FP  ATOM_FPP ]  "
> (procedure "refmac5_task_window" line 97)
> invoked from within
> "refmac5_task_window refmac5_T347B1L"
> ("eval" body line 1)
> invoked from within
> "eval "$cmd""
> (procedure "RunTask" line 109)
> invoked from within
> "RunTask refmac5"
> invoked from within
> ".module.menu.action.canvas.frame.t.f_5 invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .module.menu.action.canvas.frame.t.f_5"
> (command bound to event)
> ==
> 
> And the shell prints out:
> 
> ERROR no type for TWINREF_TYPE
> ERROR no type for F+
> ERROR no type for F-
> ERROR no type for WAVELENGTH
> ==
> 
> This is CCP4 6.1.2 on linux.  Does anyone have any ideas on what is going
> wrong?  I see one similar message in the archives, but there were no
> responses at that time.
> 
> Thanks.
> 
> -ben
> 
> --
> | Ben Eisenbraun  | Software Sysadmin  |
> | Structural Biology Grid | http://sbgrid.org  |
> | Harvard Medical School  | http://hms.harvard.edu |
-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
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*   Fax: +44 1925 603825Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] Data harvesting file corrupted in refmac

[martyn . winn]

Comparing to one of my refmac jobs, it is slightly different because of 
different system and options. However, I would guess that the missing labels 
are:

r_nbd_refined 
r_nbd_other 
r_nbtor_refined   
r_nbtor_other
r_xyhbond_nbd_refined 
r_xyhbond_nbd_other

But don't take my word for it - check it!  The numbers should correlate with 
the "Restraint type" section in the log file. Look at the last instance of 
this, since non-bonded restraint counts get updated through the refinement.

Cheers
Martyn

-Original Message-
From: CCP4 bulletin board on behalf of Yu Wai Chen
Sent: Wed 11/18/2009 11:43 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Data harvesting file corrupted in refmac
 
Dear All,

I was trying to upload a refmac-generated deposit file to PDB Autdep but 
it says the format is invalid.  So I opened the file and have a look.  
In it I saw a number of lines with ... which I suspect was the 
cause of error.  It looks like it is corrupted.  Does anyone know why it 
happened?  It seems the numeric values in these lines are all there and 
it is just the data labels that are corrupted/missing.  Is there an easy 
way I can find out the missing data field names (and the correct order) 
that I can edit them into the deposit file without re-running refmac?

The affected lines (section) are the following:

+

loop_
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
r_bond_refined_d   6700.0290.022
r_bond_other_d 4670.0010.020
r_angle_refined_deg9052.2882.000
r_angle_other_deg 11583.1133.000
r_dihedral_angle_1_deg  806.3515.000
r_dihedral_angle_2_deg  27   33.598   24.815
r_dihedral_angle_3_deg 141   14.992   15.000
r_dihedral_angle_4_deg   4   22.156   15.000
r_chiral_restr 1110.2760.200
r_gen_planes_refined   6880.0100.021
r_gen_planes_other 1200.0020.020
   1150.2990.200
   4110.1890.200
   2920.1680.200
   3060.0950.200
670.2690.200
 70.2180.200
r_symmetry_vdw_other110.1470.200
130.2730.200
r_mcbond_it4022.5761.500
r_mcbond_other 1581.1711.500
r_mcangle_it   6703.5532.000
r_mcangle_other5321.7452.000
r_scbond_it2685.4233.000
r_scbond_other 3091.9323.000
r_scangle_it   2357.4104.500
r_scangle_other6263.7704.500
r_sphericity_free  108   20.1265.000
r_sphericity_bonded   11305.5665.000
r_rigid_bond_restr11372.4793.000


+

I am running refmac ver. 5.5.0072.   Thanks in advance.

Wai

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Re: [ccp4bb] refmac

[martyn . winn]

Described at:
http://www.ccp4.ac.uk/dist/html/refmac5/keywords/xray-principal.html#scal

Simple scaling doesn't take into account the bulk solvent at all, whereas 
Babinet is a simple fix. A more sophisticated treatment of bulk solvent is 
given by the SOLVENT keyword:
http://www.ccp4.ac.uk/dist/html/refmac5/keywords/xray-principal.html#solv
which generates a solvent mask and calculates a contribution to Fcalc from that.

In the GUI, this is the "Calculate the contribution from the solvent region" 
button in the Scaling folder. By default this is on, and scaling type is 
SIMPLE. 

In principle, Babinet scaling and solvent mask calculation are alternative 
treatments of bulk solvent. There was a time however when it seemed to be 
better to use both (presumably not as bad as it sounds because scale factors 
will adjust for double counting). I think that's no longer true, but its always 
possible to "suck it and see" ...

The bottom line: if you've run with defaults, it's probably ok. With high 
solvent content, you certainly need to model the solvent one way or the other!

Cheers
Martyn

-Original Message-
From: CCP4 bulletin board on behalf of Alexandra Deaconescu
Sent: Thu 11/19/2009 3:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] refmac
 
Hi everyone:

Can someone enlighten me as to the difference between "simple" scaling  
and "Babinet scaling" in Refmac? It seems to me that Babinet scaling  
is more similar to what is employed in CNS for bulk solvent correction  
(Ksolv, Bsolv search). Is that correct? Would you recommend the  
Babinet method for high solvent content/ low resolution structures?

Thanks a lot,
Alex

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Re: [ccp4bb] converting .cv to mtz

[martyn . winn]

Your format string works for me. It's hard to say what has gone wrong without 
seeing how you ran it. Perhaps you could send me the complete log file?

If you choose column type X X-plor Rfree, then it should convert automatically 
between the conventions.

HTH
Martyn

-Original Message-
From: CCP4 bulletin board on behalf of Alexandra Deaconescu
Sent: Tue 11/17/2009 5:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] converting .cv to mtz
 
Hello:

I am switching from CNS to Refmac for refinement, and given that my FORTRAN 
classes were such a long time ago, I am having problems with the conversion. 
This is the format I give ccp4 (skipped the first 7 lines)


'(6X,3F5.0,6X,F10.3,6X,F10.3,6X,F9.3/26X,F10.3,6X,F9.0)'

and here is the beginning of my .cv

NREFlection= 20349
 ANOMalous=FALSe { equiv. to HERMitian=TRUE}
 DECLare NAME=IOBS   DOMAin=RECIprocal   TYPE=REAL END
 DECLare NAME=SIGI   DOMAin=RECIprocal   TYPE=REAL END
 DECLare NAME=FOBS   DOMAin=RECIprocal   TYPE=REAL END
 DECLare NAME=SIGMA  DOMAin=RECIprocal   TYPE=REAL END
 DECLare NAME=TEST   DOMAin=RECIprocal   TYPE=INTE END
 INDE 006 IOBS= 0.100 SIGI= 0.100 FOBS= 0.320
   SIGMA= 0.320 TEST= 0
 INDE 00   15 IOBS=  1317.300 SIGI=92.7
  

The error I get is:

List  reflection:0
  Symmetry to be listed
>> CCP4 library signal mtz:MTZ header is corrupted: missing tokens in 
>> SYMINF record (Error)
 raised in MtzGet <<
Error: failed to open file for read!
 
 ***  Error
 Error reading in HKLIN
 MTZDUMP:  *** Program Terminated 
Times: User:   0.0s System:0.0s Elapsed: 0:00  



***
* Information from CCP4Interface script
***
The program run with command: /gware/ccp4-6.1.2/linux/bin/mtzdump HKLIN 
"/scratch/deacona/ALS_Aug09_290_1_mtz.tmp" 
has failed with error message

How can I fix this? Also, I just realized that I am running also into the 
problem that in CNS the test set has Rflag of 1 and in ccp4 it is 0. Is there a 
way to go around this? I realize that you can also assign 0 to the test set in 
CNS, but the .cv file has already been made, and I do not know how to easily 
edit it to convert the Rfreeflag to the ccp4 convention.

I have also tried using the CUT pl script, but it seems it does not work (I did 
make it into an executable)

Thanks a lot,
Alex


-- 
Alexandra M. Deaconescu, Ph.D.
Damon Runyon Cancer Research Foundation Postdoctoral Fellow
Grigorieff Laboratory
Brandeis University
Rosenstiel Center
415 South St. MS-029
Waltham, MA 02454

For deliveries:

c/o Grigorieff Laboratory
Brandeis University
415 South St.
Kalman Receiving Dock
Waltham, MA 02454

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Re: [ccp4bb] edit mtz cell in header?

[martyn . winn]

Well, yes, that's how I would do it (but with Emacs). 
But I guess the official way would be with Reflection Data Utilities -> Edit 
MTZ Datasets which will edit the dataset cells. It wraps keywords of CAD.

Martyn

-Original Message-
From: CCP4 bulletin board on behalf of Ed Pozharski
Sent: Fri 11/13/2009 9:25 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] edit mtz cell in header?
 
You may be able to open mtz files in a primitive text editor such as
nano (I just did).  It's a little awkward, as there are no line breaks.
MTZ header is in the end of the file and it is plain text, so should be
easy to edit manually - just make sure you don't introduce extra space.

There are plenty of hex editors out there:

http://en.wikipedia.org/wiki/Comparison_of_hex_editors


On Fri, 2009-11-13 at 15:52 -0500, Matt Warkentin wrote:
> Howdy folks
> 
> I'm having an infuriating problem with an mtz file and sftools.  I'm
> sure this is an easy fix.  Here's the situation:  phaser gave me an
> mtz and pdb file with bad cell information.  It's I213, but the cell
> is listed as
> 
> 168.981 168.981 168.982
> 
> i.e. NOT cubic - this creates an error with my crystallography
> software downstream (buster-TNT)
> 
> So this looks like a bug in phaser, but I'm not worried about solving
> that problem right now, I just want to go in and manually change the
> cell info so its correct.  This was easy for the pdb file obviously
> because its ASCII, but the mtz is binary and requires the use of
> programs that know how to read the header info.  So I found sftools,
> which is the program to use for that right?
> 
> Within sftools, I said
> 
> READ blah.mtz
> 
> LIST CELL - at this point the incorrect cell was listed
> 
> SET CELL
> 168.981 168.981 168.981 - at this point the correct cell was listed
> 
> LIST CELL - just to be sure, yes the correct cell is listed
> 
> WRITE fixed.mtz
> 
> QUIT
> 
> Now, when I go open the new mtz file with my crystallography software,
> it still complains and reports the incorrect cell.
> 
> If I open fixed.mtz with sftools and LIST CELL it also reports the
> incorrect cell.
> 
> So it looks like sftools is not saving the correct cell to the mtz
> file.  Any thoughts?  Is there another way to change that header?
> 
> thanks
> matt
-- 


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Re: [ccp4bb] pdbcur failed with the error message 'child process exited abnormally'

[martyn . winn]

The big problem here is that it doesn't recognise the NOANISOU
keyword. So I presume that you are picking up an old version of
CCP4, or more likely a Coot version of pdbcur. Mmmm the fact that
the banner doesn't report user or date or time suggests a dodgy
version.

I would have to defer to a Mac person on how to set this up 
properly. I guess you should do a "which pdbcur" in a terminal
window to confirm the problem, and then fix your PATH somehow.

As Fred says, it is much easier to use "grep -v ANISOU foo.pdb" and I
believe you can do this even on a Mac :)

Martyn

-Original Message-
From: CCP4 bulletin board on behalf of Raja Dey
Sent: Sat 10/10/2009 12:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] pdbcur failed with the error message 'child process exited 
abnormally'
 
Hello,
I remember PDBCUR was running before updating CCP4 to 6.1.1 in my 
macbook. I am trying to remove the aniso U's from a pdb file and I stuck. I 
might need some additional setup for this to run. Is there anyone who can tell 
what to do? I attached the error message below:
   
###
 ###
 ###
 ### CCP PROGRAM SUITE: pdbcur  ##
 ###
 User:   Run date:   Run time:


 Please reference: Collaborative Computational Project, Number 4. 1994.
 The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.

 PDB file /Users/rajadey/yong/cns/alternate/final/phenix/may21_1_1_001.pdb has 
been read in.

 --
  Input cards

Data line--- NOANISOU
Unrecognised keyword "NOANISOU"
***
* Information from CCP4Interface script
***
The program run with command: pdbcur XYZIN 
"/Users/rajadey/yong/cns/alternate/final/phenix/may21_1_1_001.pdb" XYZOUT 
"/Users/rajadey/yong/cns/alternate/final/phenix/may21_pdbset1.pdb" 
has failed with error message
child process exited abnormally


Thanks... Raja


  Try the new Yahoo! India Homepage. Click here. http://in.yahoo.com/trynew

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Re: [ccp4bb] Problem in MAKE_U_POSITIVE

[Martyn Winn]

This means that some U tensors are non-positive definite (i.e. no nice
thermal ellipsoid). If by transient, you mean they have gone away by the
last cycle of refinement, then you can maybe ignore them. But probably,
you need to adjust your restraints, e.g. the SPHEricity restraint (under
Geometric parameters in the gui).

HTH
Martyn

On Wed, 2009-09-02 at 19:26 -0700, Bernhard Rupp wrote:
> Hi there – 
> 
>  
> 
> a transient message appears during anisotropic refinement 
> 
> CCP4 6.1: Refmac_5.5.0071
> 
> Problem in MAKE_U_POSITIVE
> 
> that seems to have no further consequences. I guess that means that
> some
> 
> elements in a U tensor lead to a divergent behavior, but details evade
> me. 
> 
>  
> 
> Just curious….
> 
> BR
> 
>  
> 
> -
> 
> Bernhard Rupp
> 
> b...@ruppweb.org
> 
> http://www.ruppweb.org/ 
> 
> -
> 
> Anything is possible if you don't know 
> 
> what you are talking about.
> 
> -
> 
> 
> 
>  
> 
> 
-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603825Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] anisotropic temp for H2O

[Martyn Winn]

In the latest versions of refmac, it has a default selection of TLS
groups so that you don't need to create a TLSIN file. I believe this
default selection includes waters in the first hydration shell. You
should be able to override this with an explicit selection in TLSIN.

Cheers
Martyn

On Thu, 2009-08-27 at 09:37 -0700, Ethan Merritt wrote:
> On Thursday 27 August 2009, Elad Binshtien wrote:
> > Dear all,
> > I run refmac5 on TLS & restrained refinement mode. my pdb input file 
> > contain anisotropic temp for the amino acid and isotropic temp for the 
> > cofactors and water. The refinement parameters is set on mixed isotropic/ 
> > anisotropic temp and in TLS parameters the check box add TLS contribution 
> > is marked. 
> 
> But in your definition of TLS groups  (the *.tls input file)
> do you list the water residues as belonging to one of the TLS groups?
> If so, don't do that.
> 
>   Ethan
> 
> 
> > In the pdb output the cofactor stay with isotropic temp BUT the water get 
> > anisotropic temp.
> > How can i leave the water with the isotropic tepm
> > (i work on win version) 
> > 
> > thanks Elad
> > 
> > 
> > 
> > Elad Binshtein
> > Ph.D student 
> > Department of Life Science 
> > Ben Gurion University of the Negev
> > Ph: 972-8-6461325‎
> > 
-- 
*******
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603825Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] How to work around strange naming XYZIN convention?

[Martyn Winn]

You should be able to do this kind of scripting.

The CCP4 library will try to add an extension, iff there is not one
already. But if you have set $tempfile to "foo.pdb" then it shouldn't
add anything. 

Code is in ccp4_general.c if you want to sabotage it ...

The list of default extensions is in $CCP4/include/environ.def
(but we obviously need to update .brk to .pdb)

HTH
Martyn

On Mon, 2009-08-24 at 17:30 -0700, Ethan Merritt wrote:
> Not sure this is the right place to ask, but...
> 
> I'm trying to chain some ccp4 programs together via a script.
> It creates temporary files with arbitrary names based on the process id.
> The problem is that when I try to pass one of these files to the
> next program in the chain, as in:
> 
>tlsanl XYZIN $tempfile <...
>EOF
> 
> The ccp4 libraries seem to expand this to be an input file named
>$tempfile.brk
> 
> Is there any way to make the programs _not_ append a useless extension
> ".brk"  in a scripted environment?
> 
-- 
***
*     *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603825Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

[ccp4bb] CCP4 at the ECM

[Martyn Winn]

Hi all,

CCP4 staff, developers, collaborators and assorted hangers-on will be at
the ECM in Istanbul from this Sunday. We will have a stand in the
Exhibition, where we will be available to help or generally talk to. I
am told that we are booth number 34, though at the moment I have no idea
where that is  I am assuming all will become clear by Monday
morning.

There should be somebody at the stand for most of the breaks and during
the afternoon poster session. We will try to organise specific times for
demonstrations or guest developers - we'll post information on the
stand. 

For reasons beyond our control (or at least wit), we won't have much
stuff at the booth. So if anyone has ideas to brighten us up, please let
us know. Anyone making a contribution will receive a free bug fix.

See you there,
Martyn

-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603825Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] Reporting crashes to CCP4BB...

[Martyn Winn]

I put this link on the CCP4 web pages some time ago, but it is probably
worth repeating:

http://www.catb.org/~esr/faqs/smart-questions.html

I think the crucial insight is that the psychic abilities of developers
are often over-estimated :P

m


On Fri, 2009-07-31 at 10:57 +0100, Kevin Cowtan wrote:
> Hi!
> 
> We've had a few program crashes reported to the BB and by email 
> recently, and working out what is going on can be quite difficult and 
> time consuming.
> 
> It is useful to consider when writing such a report how interested you 
> are in receiving a helpful answer. If you just want us to know that our 
> software isn't perfect, then a message saying 'program X crashes' is 
> fine (although some of us know that already). If you want to know how to 
> get the software to work with your data, then you will probably have to 
> provide a little more information.
> 
> Here's a rough table of how likely you are to get a solution based on 
> how much information you provide:
> 
> Message:--Chance of solution:
> 
> It crashes!---Zero
> It crashes with message X-Slim
> Last 20 lines of the logfile--Poor
> Whole logfile-Moderate to good
> 
> Of course you might not want to send the whole log file to the bulletin 
> board. In this case, you can always send a censored or shortened version 
> to the bulletin board and send more information to any developer who 
> asks. In the hardest cases, the developer may need access to your data, 
> which you may or may not be able to provide of course.
> 
> Hope that helps!
> Kevin
> 
-- 
*******
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603825Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

Re: [ccp4bb] ccp4i, OS X 10.5.7, & security enforcement

[Martyn Winn]

This code hasn't changed since 2000, and I think we would have noticed
if there was something fundamentally wrong with it. So before going off
on a long analysis of shell scripting, it is best to check basics. 

What have you changed? You have added an "echo" statement. Why should
that matter? Because the previous line ends in a continuation marker, so
you have changed what follows that.

Now this seems to be fairly obscure (to me as well, not my code).
http://wiki.tcl.tk/812 has some notes on the "continuation-line trick".
That article does suggest that it is deprecated, but I'd be loathe to
"fix" something which apparently works for thousands of users.

I guess the question is why did you insert the echo statement? Were you
trying to fix another problem?

I am also unclear what the connection to injection attacks is?

Cheers
Martyn

On Sun, 2009-07-26 at 14:34 -0700, James Stroud wrote:
> Hello All,
> 
> It seems that sh has a variable that exists and doesn't exist at the  
> same time (see my shell session below). Isn't such transition between  
> existence and non-existence reserved for quantum mechanics and eastern  
> philosophy? My guess is that sh has become more vigilant about  
> security and the exec statement. Can anyone venture a better guess as  
> to how the output below might happen?  What's the best way around  
> this? But the real question is: Can the people at ccp4 look at this  
> and make changes to the code base before these kinds of security  
> features become more commonplace (for the good reason to prevent  
> injection attacks)?
> 
> For example: 
> http://www.theregister.co.uk/2009/07/21/critical_ddwrt_router_vuln/
> 
> Here is my shell session:
> 
> chernev 10% cat `which ccp4i`
> #!/bin/sh
> # Start ccp4i interface
> # \
> echo CCP4I_TCLTK is $CCP4I_TCLTK
> exec ${CCP4I_TCLTK}/bltwish "$0" -- ${1+"$@"}
> source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
> chernev 11%
> chernev 12% ccp4i
> CCP4I_TCLTK is /usr/local/X11/bin
> Error in startup script: can't read "CCP4I_TCLTK": no such variable
>  while executing
> "exec ${CCP4I_TCLTK}/bltwish "$0" -- ${1+"$@"}"
>  (file "/usr/local/ccp4-6.1.1/bin/ccp4i" line 5)
-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603825Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

[ccp4bb] Research technician at oxford University

[Martyn Winn]

Posted on behalf of Dina Fotinou (so don't reply to me, follow the
instructions):



Research Technician required to support the
protein expression and purification project in a
group led by Professor Frances Ashcroft which is
studying the ATP-sensitive potassium (KATP)
channel and its role in insulin secretion in
health and disease.

Further particulars are available from:
http://www.dpag.ox.ac.uk/job_opportunities/AV09014

Informal enquiries may be addressed to
Prof.Ashcroft:

frances.ashcr...@dpag.ox.ac.uk


-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603825Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***