Re: [ccp4bb] proxy settings for ccp4 package manager

[Takanori Nakane]

Hi Johannes,

On RHEL 6.7, setting "http_proxy" was sufficient.

Best regards,

Takanori Nakane

On 2018/01/09 13:18, Johannes Cramer wrote:

Dear CCP4bb,

does anyone know how I can make the ccp4 package manager use a proxy for
downloading in Linux 64bit versions?
This would make installing and updating a whole lot easier for me...

I exported http_proxy, https_proxy, ftp_proxy (and all their capital letter
equivalents) and setup the system proxy in kde (although I think this only
matters for kde programs). I am using the 10.17 version of kubuntu, but
would also be interested in a solution that works for Mac.

Cheers,
Johannes

Re: [ccp4bb] reindexing mtz

[CCP4BB]

Sorry - my bad memory and mis-reading the manual...

Harry
--
Dr Harry Powell
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

> On 10 Jan 2018, at 21:30, Phil Evans  wrote:
> 
> I don’t think Pointless can (or should) read .x files - they have to go into 
> scalepack as that sorts out various things in the data. Pointless can read 
> unmerged .sca files from scalepack, but they can’t be (properly) scaled in 
> Aimless
> 
> Phil
> 
>> On 10 Jan 2018, at 21:11, CCP4BB 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hi Peter
>> 
>> No, don't bother scaling in hkl2000.
>> 
>> Just take the .x files and read them into Pointless directly - it should 
>> auto-detect the file type and any output reflection file from it will be in 
>> MTZ format. Then Aimless can do the scaling. 
>> 
>> See the manual, e.g. 
>> 
>> https://www.mrc-lmb.cam.ac.uk/harry/pre/pointless.html
>> 
>> for details.
>> 
>> You should be able to do this in ccp4i2 as well.
>> 
>> If you use the already merged reflections for reindexing, there's a chance 
>> that reflections that are not equivalent will have been merged.
>> 
>> Harry
>> --
>> Dr Harry Powell
>> Chairman of European Crystallographic Association SIG9 (Crystallographic 
>> Computing) 
>> 
>>> On 10 Jan 2018, at 18:58, Peter Hsu  wrote:
>>> 
>>> Just to be absolutely clear about my approach to doing this, I should scale 
>>> in HKL2000 as an unmerged set, and then take the unmerged scalepack, 
>>> convert to mtz and run through pointless? 
>>> 
>>> Also, would taking my current mtz (which is a merged dataset) work using 
>>> the reindex program in CCP4? Are there any pitfalls I need to be aware of? 
>>> 
>>> Apologies for the ignorance.
>>> 
>>> Thanks,
>>> Peter

Re: [ccp4bb] reindexing mtz

[Phil Evans]

I don’t think Pointless can (or should) read .x files - they have to go into 
scalepack as that sorts out various things in the data. Pointless can read 
unmerged .sca files from scalepack, but they can’t be (properly) scaled in 
Aimless

Phil

> On 10 Jan 2018, at 21:11, CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi Peter
> 
> No, don't bother scaling in hkl2000.
> 
> Just take the .x files and read them into Pointless directly - it should 
> auto-detect the file type and any output reflection file from it will be in 
> MTZ format. Then Aimless can do the scaling. 
> 
> See the manual, e.g. 
> 
> https://www.mrc-lmb.cam.ac.uk/harry/pre/pointless.html
> 
> for details.
> 
> You should be able to do this in ccp4i2 as well.
> 
> If you use the already merged reflections for reindexing, there's a chance 
> that reflections that are not equivalent will have been merged.
> 
> Harry
> --
> Dr Harry Powell
> Chairman of European Crystallographic Association SIG9 (Crystallographic 
> Computing) 
> 
> On 10 Jan 2018, at 18:58, Peter Hsu  wrote:
> 
>> Just to be absolutely clear about my approach to doing this, I should scale 
>> in HKL2000 as an unmerged set, and then take the unmerged scalepack, convert 
>> to mtz and run through pointless? 
>> 
>> Also, would taking my current mtz (which is a merged dataset) work using the 
>> reindex program in CCP4? Are there any pitfalls I need to be aware of? 
>> 
>> Apologies for the ignorance.
>> 
>> Thanks,
>> Peter

Re: [ccp4bb] reindexing mtz

[CCP4BB]

Hi Peter

No, don't bother scaling in hkl2000.

Just take the .x files and read them into Pointless directly - it should 
auto-detect the file type and any output reflection file from it will be in MTZ 
format. Then Aimless can do the scaling. 

See the manual, e.g. 

https://www.mrc-lmb.cam.ac.uk/harry/pre/pointless.html

for details.

You should be able to do this in ccp4i2 as well.

If you use the already merged reflections for reindexing, there's a chance that 
reflections that are not equivalent will have been merged.

Harry
--
Dr Harry Powell
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

> On 10 Jan 2018, at 18:58, Peter Hsu  wrote:
> 
> Just to be absolutely clear about my approach to doing this, I should scale 
> in HKL2000 as an unmerged set, and then take the unmerged scalepack, convert 
> to mtz and run through pointless? 
> 
> Also, would taking my current mtz (which is a merged dataset) work using the 
> reindex program in CCP4? Are there any pitfalls I need to be aware of? 
> 
> Apologies for the ignorance.
> 
> Thanks,
> Peter

Re: [ccp4bb] reindexing mtz

[Peter Hsu]

Just to be absolutely clear about my approach to doing this, I should scale in 
HKL2000 as an unmerged set, and then take the unmerged scalepack, convert to 
mtz and run through pointless? 

Also, would taking my current mtz (which is a merged dataset) work using the 
reindex program in CCP4? Are there any pitfalls I need to be aware of? 

Apologies for the ignorance.

Thanks,
Peter

Re: [ccp4bb] reindexing mtz

[Eleanor Dodson]

Thanks Paul -
Peter, in that case I think you can just read the data into pointless and
it will suggest possible spacegroups and the appropriate reindexing.

eleanor

On 10 January 2018 at 11:07, Paul Emsley  wrote:

> On 10/01/2018 10:58, Eleanor Dodson wrote:
>
>> Yes - that is possible, but need more information. Are the files unmerged
>> data?
>>
>
> .x files from hkl are unmerged data
>
>

[ccp4bb] Acta Cryst F special issue on carbohydrates

[Jon Agirre]

Dear colleagues,

just a quick update regarding the special issue with title 'Crystallography
of glycoproteins and protein-carbohydrate complexes', which Mark van Raaij
and I are co-editing for Acta Crystallographica Section F: Structural
BIology Communications.

We have extended the deadline for independent submissions until the 1st of
February. The URL for submitting papers is:
http://submission.iucr.org/submit/f?Qconf=glycoproteins

We should like to take this opportunity to thank those who have already
submitted their contributions for this issue - they are much appreciated.

Yours sincerely,

Jon & Mark


-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @alwaysonthejazz

Re: [ccp4bb] reindexing mtz

[Eleanor Dodson]

Yes - that is possible, but need more information. Are the files unmerged
data?
Eleanor

On 10 January 2018 at 03:34, Peter Hsu  wrote:

> Dear all,
>
> Looking to get some advice on reindexing an old dataset. I recently solved
> a structure of reasonable resolution at ~3A in C2. I had an old dataset at
> 4A in P213 that I never got a MR solution with until I solved the structure
> of it at 3A. I've recently gone back to to this and managed to find a
> solution using MolRep. However, I've not been able to refine the solution
> to anything below an Rfree of 60. Went back to try it in P23 and also found
> solution, but was never able to refine it.
>
> I had a suggestion from my boss to reindex in a different space group
> (I23), but I've since misplaced the original image files (terrible) and
> only have the .X files from HKL. I'm wondering if it's possible to reindex
> using either CCP4 or Phenix. I know there's a utility for it, but my
> understanding is poor and I'm not sure if I can go from P --> I using this
> program.
>
> Thanks for any input on this very dumb problem.
>
> Peter
>

[ccp4bb] CANES MSc/PhD Applications now open-September 2018 entry

[Lorenz, Chris]

Applications are now open for the CANES Programme
(September 2018 entry)
Download our poster 
here
View this email in your 
browser


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10 fully-funded 4-year PhD studentships
Additional industry-sponsored studentships possible
Apply by 19 February 2018 for September 2018 entry
(late consideration possible)

Non-equilibrium processes underpin many challenging problems across the natural 
sciences. The mission of 
CANES
 is to train a new generation of researchers in cross-disciplinary approaches 
to non-equilibrium systems, focussing on the three key strands of theoretical 
modelling, simulation and data-driven analysis. It draws on a broad range of 
supervisor expertise in Mathematics, Physics, Chemistry, Informatics, 
Computational and Systems Biomedicine, Earth and Environmental Sciences, 
including partners at Imperial College London, University College London and 
Queen Mary University of London.



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Why study within our CDT?

The training programme consists of a first year combining taught courses and 
research projects, leading to the award of an MSc. In years two to four, 
students will progress to the PhD component where the emphasis will shift to 
research. Structured training is delivered by a number of routes, which include 
open question sandpits, master classes, seminars, journal clubs and an annual 
retreat. Students will also be able to undertake internships at a broad range 
of industrial and international academic partners.

The Centre for Doctoral Training CANES offers:

  *   An innovative programme of teaching, delivered by academics with a vast 
range of expertise in non-equilibrium systems across the Faculties of Natural 
and Mathematical Sciences, Life Sciences and Medicine and Social Science and 
Public Policy.
  *   High quality training in a broad range of transferable skills, public 
engagement and outreach activities.
  *   A cohort approach to learning.
  *   Student led choice of research project.
  *   An interdisciplinary pool of supervisors directing a wide range of 
cutting-edge and challenging research projects in the rapidly developing and 
exciting field of non-equilibrium systems.

Who should apply?

Excellent undergraduates holding or expecting to gain a Bachelor’s degree (or 
equivalent international qualification) with First Class honours in a relevant 
discipline including mathematics, physics, chemistry, engineering, materials 
science, biophysics, geophysical sciences and computer science. A 2:1 (upper 
second class) honours degree (or international equivalent) may be acceptable 
depending on the candidate's academic background, including e.g. strong 
performance (predicted or achieved) in a Master's degree.

A strong background in quantitative science will be essential for students to 
take full advantage of the CANES training programme.

Funding

The Centre funds around 10 studentships each year. Each studentship is funded 
for 4 years. Funding covers:

  *   A tax-free stipend of around £16,500 per year.
  *   Tuition fees.
  *   A generous conference travel and internship fund.

The programme can support UK applicants as well as a limited number of students 
from the EU and overseas.

How to apply

For further details and how to apply visit 
http://www.kcl.ac.uk/canes

The list of potential CANES PhD projects is also available on-line; however 
please consider that more might be added around mid-January 2018 so interested 
candidates are invited to check the website regularly.

Application deadline: Interested candidates should apply by 19 February 2018. 
Applications received after this date will be considered where possible, 
particularly for candidates from outside the UK who may have later local 
deadlines.

Informal enquiries can be addressed to the CANES Centre Manager 
(ca...@kcl.ac.uk).




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Re: [ccp4bb] CCP4MG error after installation

[Stuart McNicholas]

Dear Matthew,
   Does the program fail to run, or fail to load files? The above message
may or may not be a real error. CentOS 6 should not be a problem for
ccp4mg, but I will try to check later today to see if I have the same
problem as you.

You could try the "standalone" version of ccp4mg outside of the CCP4 suite.
This will not have the MrBUMP/CCP4i2 integration, but should have all other
features. The latest version of this can be got from:

http://www.ccp4.ac.uk/MG/nightly/

Best wishes,
Stuart McNicholas


On 9 January 2018 at 19:28, Whitley, Matthew J  wrote:

> Hello all,
>
>
> After installing ccp4 7.0 and all updates via the package manager on
> CentOS 6, I receive the following error messages upon running ccp4mg:
>
>
>
> libpng error: IDAT: invalid distance too far back
> QPainter::begin: Paint device returned engine == 0, type: 2
> QPainter::end: Painter not active, aborted
>
> The path to the ccp4mg executable on our system is as follows:
>
> /usr/local/ccp4-7.0/ccp4-7.0/bin/ccp4mg
>
>
>
> I would appreciate any ideas about the source of the issue and how to
> resolve it.
>
>
>
> Sincerely,
>
> Matthew Whitley
>
>
> ---
> Matthew J. Whitley, Ph.D.
> Research Instructor
> W. Furey Lab
> Department of Pharmacology & Chemical Biology
> University of Pittsburgh School of Medicine
>

Re: [ccp4bb] Help needed to make a clue about ligand

[Allister Crow]

Shankar,

It looks like Acetyl coA to me.

Best wishes,

- Allister


> On 10 Jan 2018, at 04:09, Shankar Prasad Kanaujia  
> wrote:
> 
> Dear All,
> 
> Wishing you all a very happy and prosperous new year 2018
> 
> We have recently solved a structure which contains a huge density in the 
> active site. We modelled a molecule fitting the electron density (please see 
> the attached figures). However, we could not find any known molecule similar 
> to the fitted molecule either in PDB or PubChem databases. Thus, we are not 
> able to correlate its existence in cell.
> 
> The protein was expressed in E. coli cells. The structure is solved at 1.85 
> Angst. We have not added any molecule like this in any step of the 
> experiments.
> 
> Looking forward to having some ways to figure out this problem.
> 
> With best regards,
> Shankar
> 
> 
> -- 
> Shankar Prasad Kanaujia, Ph.D.
> Associate Professor
> Department of Biosciences and Bioengineering
> Indian Institute of Technology Guwahati
> Guwahati - 781039 Assam, India
> Tele: 0361 258 2228
> Fax:  0361 258 2249
> Email: spkanau...@iitg.ernet.in 
> Homepage: http://www.iitg.ernet.in/spkanaujia/ 
> 
> Google Scholar: https://scholar.google.com/citations?user=Zt4JSNYJ=en 
> 
> 

-
Allister Crow
School of Life Sciences
University of Warwick

[ccp4bb] iNEXT annual user meeting Grenoble, 19-21 March 2018

[Darren Hart]

*Announcement of the iNEXT Annual User Meeting in Grenoble*

The* 3**^rd **Annual Users Meeting of iNEXT* will take place from 
*19*^*th * *to 21*^*st* * March 2018*at the European Photon and Neutron 
(EPN) Science campus in *Grenoble (France)*. The EU-funded structural 
biology project *iNEXT* provides free user access to some of the most 
advanced facilities for structural biology in Europe: X-ray synchrotron 
sources, high-field NMR facilities, Electron Microscopy, and other 
imaging and biophysical characterization facilities.


The meeting is intended to bring together iNEXT users and iNEXT partners 
to exchange on recent scientific advances made in the field of 
structural biology. A large part of the meeting is devoted to scientific 
presentations in various fields of structural biology


Confirmed speakers of this scientific meeting include *Christian 
GRIESINGER, *(MPI for Biophysical Chemistry, Göttingen, Germany), *Maria 
SUNNERHAGEN (*Linköbing University, Sweden),*Chris ULENS (*Laboratory of 
Structural Neurobiology,**Leuven, Belgium), *Ilme SCHLICHTING *(MPI for 
Medical Research, Heidelberg, Germany), and *Jürgen PLITZKO (*MPI for 
Biochemistry, Martinsried, Germany). Additional speakers will be 
selected from the submitted abstracts.



*Registration to the event (including lodging on-site and meals) is free 
of charge.***Additional information on the iNEXT AUM meeting 2018 and 
registration at: http://www.esrf.eu/inext-annual-users-meeting-2018.


Deadline for registration is *February**5*^*th* .

The 3^rd  Annual Users Meeting will be followed by a dedicated“*iNEXT 
meets Industry*” workshop 
from 21^st to 23^rd 
 March at the same place (EPN campus, Grenoble).



See also:

http://www.inext-eu.org/3rd-inext-annual-user-meeting-in-grenoble-registration-is-open/