Re: [ccp4bb] nVidia 3D Vision2 glasses

[Weiergräber, Oliver H.]

Note that the more recent versions of EL7 no longer require compositing to be 
disabled for nVidia stereo to work with Gnome3.

Cheers,
Oliver

==
  PD Dr. Oliver H. Weiergräber
  Institute of Biological Information Processing
  IBI-7: Structural Biochemistry
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540
==

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of David J. 
Schuller [schul...@cornell.edu]
Sent: 14 January 2020 22:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] nVidia 3D Vision2 glasses

Which Linux and which desktop?

Attached find a typical functional /etc/X11/xorg.conf file for stereo use from 
a Scientific Linux 7 machine.
The two notable things about this file:
"STEREO" is enabled in the "Screen" section.
"COMPOSITE" is disabled in the "Extensions" section.

With some newer desktops such as Gnome 3 it is not possible to disable 
composite. Try using the XFCE or Mate desktop.



On 2020-01-14 15:43, Oganesyan, Vaheh wrote:
Colleagues,
While on stereo issues here is problem I’m trying to resolve with community 
help:
my hardware includes nVidia quadro FX1400, Xpand emiter and NewVision glasses. 
Driver taken from nVIDIA site specifically for Quadro FX 1400, long lived. On 
old Linux station these worked together fine for PyMOL and O. On newer machine 
PyMOL doesn’t complain but doesn’t show stereo either. “O” complains:


freeglut (/home/Vaheh/o/bin/170211_lin64_ono): ERROR: Internal error  in function fgOpenWindow

and quits.

Will appreciate help on resolving this issue.


Regards,

Vaheh Oganesyan, Ph.D.
Scientist, Biologic Therapeutics

AstraZeneca
R | Antibody Discovery and Protein Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
vaheh.oganes...@astrazeneca.com




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



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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt





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[ccp4bb] Postdoctoral Position in Structure and Function of GPCRs at Wash. U.

[Krumm, Brian]

Posted on behalf of a colleague, please respond directly to the e-mail
address below.


*Postdoctoral Position in Structure and Function of G protein-coupled
Opioid Receptors and Other Pain-related Targets.*



A postdoctoral position is available in the research group of Tao Che,
Department of Anesthesiology, Washington University in St. Louis, Missouri.
Employment will commence tentatively in early Summer 2020, exact starting
date is negotiable.



*The long term goal of the Che lab is to understand the structure, function
and pharmacology of pain-related G protein-coupled receptors (GPCRs),
particularly opioid receptors.* Opioid receptors are GPCRs whose role in
pain sensation has made them major drug targets for pain medications such
as oxycodone and morphine. However, opioids have exceptionally high abuse
potential and often cause fatal side effects such as respiratory arrest and
death. *Towards a molecular understanding of opioid receptor signaling, we
employ a combination of state-of-the-art structural (X-ray crystallography,
cryo-EM) and pharmacological techniques to gain an atomic-level
understanding of opioid receptor activation (Cell, 2018), **and leverage
these data using structure-based drug design to develop novel therapeutics
(Nature, 2018).*



Applicants should hold a PhD in a relevant subject area, such as protein
biochemistry, structural biology or pharmacology. Structure determination
using x-ray crystallography and/or cryo-EM along with functional analysis
using biochemical, biophysical and pharmacological techniques would be a
plus. The ability to work in a team, as well as good communication skills,
are expected.



Applications that include a brief description of research interests, as
well as a CV with contact information of three references should be sent to:
tao...@wustl.edu

Tao Che, PhD

Assistant Professor

Department of Anesthesiology

Washington University in St. Louis

St. Louis, MO 63110



Che Google Scholar:
https://scholar.google.com/citations?user=DrcnS4sJ=en


The Che lab is located in the School of Medicine campus. In the latest
(2019) rankings by USNEWS, Wash U ranks #8 in Anesthesiology and #8 in Medical
School (research). Washington University School of Medicine (WUSM) has a
brand-new fully-functional FEI Titan Krios cryo-EM and is dedicated to
biological applications.



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Re: [ccp4bb] nVidia 3D Vision2 glasses

[David J. Schuller]

Which Linux and which desktop?

Attached find a typical functional /etc/X11/xorg.conf file for stereo use from 
a Scientific Linux 7 machine.
The two notable things about this file:
"STEREO" is enabled in the "Screen" section.
"COMPOSITE" is disabled in the "Extensions" section.

With some newer desktops such as Gnome 3 it is not possible to disable 
composite. Try using the XFCE or Mate desktop.



On 2020-01-14 15:43, Oganesyan, Vaheh wrote:
Colleagues,
While on stereo issues here is problem I’m trying to resolve with community 
help:
my hardware includes nVidia quadro FX1400, Xpand emiter and NewVision glasses. 
Driver taken from nVIDIA site specifically for Quadro FX 1400, long lived. On 
old Linux station these worked together fine for PyMOL and O. On newer machine 
PyMOL doesn’t complain but doesn’t show stereo either. “O” complains:


freeglut (/home/Vaheh/o/bin/170211_lin64_ono): ERROR: Internal error  in function fgOpenWindow

and quits.

Will appreciate help on resolving this issue.


Regards,

Vaheh Oganesyan, Ph.D.
Scientist, Biologic Therapeutics

AstraZeneca
R | Antibody Discovery and Protein Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
vaheh.oganes...@astrazeneca.com




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



To unsubscribe from the CCP4BB list, click the following link:
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# /etc/X11/nvidia-xorg.conf provided by http://elrepo.org

Section "Device"
Identifier  "Videocard0"
Driver  "nvidia"
EndSection
Section "Monitor"
Identifier   "Monitor0"
VendorName   "Planar"
ModelName"SA2311W"
HorizSync30.0 - 140.0
VertRefresh  56.0 - 120.0
Option  "DPMS"
EndSection
Section "Screen"
Identifier "Screen0"
Device "Device0"
Monitor"Monitor0"
DefaultDepth 24
Option "Stereo" "10"
SubSection "Display"
Modes  "1920x1080" "1920x1080_120"
Depth 24
EndSubSection
EndSection

Section "Extensions"
Option "COMPOSITE" "Disable"
EndSection




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[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

MoRDa is a pipeline for molecular replacement structure solution.

A new update to the package is now available. The structure solution program is 
improved and database is extended .

Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Also Morda at ccp4online  has been updated. 

Best regards
Alexey




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Re: [ccp4bb] nVidia 3D Vision2 glasses

[Oganesyan, Vaheh]

Colleagues,
While on stereo issues here is problem I’m trying to resolve with community 
help:
my hardware includes nVidia quadro FX1400, Xpand emiter and NewVision glasses. 
Driver taken from nVIDIA site specifically for Quadro FX 1400, long lived. On 
old Linux station these worked together fine for PyMOL and O. On newer machine 
PyMOL doesn’t complain but doesn’t show stereo either. “O” complains:


freeglut (/home/Vaheh/o/bin/170211_lin64_ono): ERROR: Internal error  in function fgOpenWindow

and quits.

Will appreciate help on resolving this issue.


Regards,

Vaheh Oganesyan, Ph.D.
Scientist, Biologic Therapeutics

AstraZeneca
R | Antibody Discovery and Protein Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
vaheh.oganes...@astrazeneca.com




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[ccp4bb] PhD studentship (UK): Dynamic Structural Biology – from nanocrystals to time-resolution (CASE project)

[Patrick Shaw Stewart]

The South Coast Biosciences (SoCoBio) Doctoral Training Partnership is
offering a PhD student a unique opportunity to undertake research and
training in structural biology and microfluidics.

https://research.kent.ac.uk/socobio/dynamic-structural-biology-from-nanocrystals-to-time-resolution/



Primary supervisor:
Dr Ivo Tews, Biological Sciences, University of Southampton
Co-supervisors:
Dr S. Mark Roe, School of Life Sciences, University of Sussex
Dr Jonathan West, Medicine, University of Southampton

Project Summary

Significant technical developments are revolutionising structural biology
and change the way in which a crystallographic experiment is approached.
Noise-free detection, advances in synchrotron X-ray sources and
availability of pulsed X-ray free electron laser sources (XFEL) now firmly
establish serial crystallography. Thousands of nanocrystals each contribute
a single x-ray exposure. The method is able to add dynamic information on
structural changes or transitions, observed over time. Enzymes or higher
order molecular complexes are prominent targets.

Micro- or nanocrystalline samples are required to unlock this capability.
We developed a workflow for optimising crystal growth for size and
homogeneity [1] and demonstrated serial data collection with a fixed target
delivery approach using a nano-fabricated chip-based support system,
capable of delivering one structure per hour either at the Diamond Light
Source (I24 microfocus beamline) or at an XFEL source (SACLA, Japan).

The PhD will optimise nano-crystallisation to study two high value targets.
Micro-seeding approaches are developed in collaboration with the highly
innovative CASE partner Douglas Instruments [2]. Novel high-throughput
approaches in nano-crystallisation using microfluidic platforms are
developed at Southampton [3].

*Target 1: Hsp90, a chaperone implicated in maintaining many cancers [4].
Very small crystals of Hsp90 in complex with co-chaperones and client
proteins can be formed (specifically the Hsp90/cdc37/Braf complex). The
size of these crystals is such that they are not suitable for standard data
collection, and serial nano-crystallography will enable structure
determination to understand how Hsp90 aids in protein maturation.*
*Target 2: Pdx1, an enzyme that synthesises vitamin B6 from two
carbohydrates and ammonia. Crystallisation of several key intermediates is
established, and the complex cascade of reactions has been described by us
[5]. Serial data collection to map the highly dynamic changes in the enzyme
is now required, investigating sugar ring opening, ammonia transfer, and
migration of intermediates.*


-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36



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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[David Lawson (JIC)]

Just to follow up on this one...

The problem was at my end, there was an issue with the upload from my iMac 
(possibly something to do with the system's proxy server settings). When I 
switched to using a PC, everything works as it should.
N.B. when providing a scaled but unmerged mtz, it is important to have the 
"Check here if the data are unmerged but already scaled ..." button checked.

Thanks to Ian and Clemens at Global Phasing for help with troubleshooting.

Dave

---

Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk

From: CCP4 bulletin board  On Behalf Of David Waterman
Sent: 14 January 2020 11:21
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

Hi Eleanor,

MTZ history is still useful, so from a recent xia2 run I can see (with mtzdmp):

 * HISTORY for current MTZ file :

 From DIALS 2.0.1-gb22bab67b-release, run on 2019-11-21 at 10:59:17 GMT

It isn't possible to tell that the data were actually scaled in DIALS too 
though, apart from the lack of POINTLESS and AIMLESS lines within the history. 
As Graeme says, I think there are opportunities here for more sophisticated 
tracking of provenance - certainly going back as far as telling us where and 
when the images were collected would be most useful.

Cheers
-- David


On Tue, 14 Jan 2020 at 11:04, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Not quite relevent but is there some way of stamping these files with a record 
of where they were generated ?
I used to use my ability to read - name them myself as
SAMPLEX-dialsprocessing-unmerged.mtz then
SAMPLEX-dialsprocessing-unmerged-staranisod.mtz

and there is an mtz feature which wrote a history with dates as well but now 
with automated file naming it is hard to keep track of how a file was generated.


It seems likely that lots of Table !s do not describe the data set that was 
actually used for structure solution and deposition!

Eleanor

On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) 
mailto:graeme.win...@diamond.ac.uk>> wrote:
Dear  Dave, Star Aniso Developers,

If this turns out to be because we are “missing something” i.e. there is an 
expectation on a property being present in the output files but it’s not there 
in our MTZ output, please let us know :-)

Best wishes Graeme


On 14 Jan 2020, at 09:06, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:

Dear ccp4bb

I am trying to get the staraniso server to accept a scaled but unmerged mtz 
file from DIALS processing, but it reports an “Internal Server Error” after 
thinking about it for a while. Should this be possible? The file is 31 MB, so 
not huge.

It works fine for a merged mtz from DIALS, but this is not the preferred option 
and I don’t get the full statistics I need for Table 1.

Thanks in advance

Dave Lawson

---

Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk




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This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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[ccp4bb] ZoBio is looking for an experienced scientist to strengthen its Structural Biology / X-ray Crystallography group in Leiden (NL)

[Denys Pogoryelov]

**
ZoBio is looking for an experienced scientist to strengthen its Structural 
Biology / X-ray Crystallography group in Leiden (NL)
**
ZoBio (www.zobio.com) was founded in 2004 and is located in Leiden, The 
Netherlands. ZoBio offers innovative research services in the field of 
small-molecule drug discovery to the pharmaceutical and biotech industries. Our 
international team of 26 people covers four fields of expertise: Protein 
Engineering and Production, Assay Development and Screening, Structural 
Biology, and Medicinal Chemistry.
We are currently looking to strengthen our team with a highly motivated X-ray 
crystallographer, with a track record in protein crystallography and with 
experience in model building and refinement of protein – small-molecule 
complexes. 
You will support our clients’ drug discovery programs by solving ligand-protein 
structures by X-ray crystallography. You will work with minimal supervision but 
in a highly collaborative environment within the Structural Biology team and 
will effectively cooperate on a per-project basis with other research groups at 
ZoBio. This role requires working on multiple projects simultaneously and in a 
rapidly evolving environment. Team spirit and excellent organization and 
communication skills are essential.
RESPONSIBILITIES 
•   High-throughput crystal preparation and optimization utilizing 
automation and robotics.
•   Data collection at synchrotron facilities. 
•   High-throughput and -quality structure elucidation and interpretation 
of biological macromolecules in complexes with small molecules of interest. 
•   Report results to the group head and prepare presentations on the 
structural data for the project teams and clients.
•   Maintain up-to-date understanding of the state-of-the-field in X-ray 
crystallography and in relation to modern drug discovery challenges.
REQUIREMENTS
•   PhD in relevant field with experience in an industrial or collaborative 
setting. 
•   Use of common structure determination software, including the CCP4 
suite and Coot.
•   Hands-on experience with ligand modelling into electron density maps, 
and macromolecular model building and refinement in the context of 
Structure-Based Drug Discovery campaigns.
•   Hands-on experience in solving challenging X-ray crystallography cases 
(e.g. ab initio structure solution).
•   Able to work in a team in a result-driven, goal-oriented environment.
It is fully expected that you will become a permanent and integral member of 
the ZoBio team, after an initial period of 12 months.
A tailored remuneration package will be proposed in line with individual 
qualifications and experience. The position is immediately available; the 
evaluation and assessment of candidates will run until the position is filled 
but not later than the end of February 2020.  

Please send your CV, motivation letter and names of potential referees at 
 with the subject: 
“Scientist position in X-ray Crystallography”.
**



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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[Ian Tickle]

Hi Graeme

No it looks like the problem is some network setting on David's side since
I can submit David's data to the STARANISO server with no problem.  The
only thing to be aware of is that when submitting scaled unmerged data the
checkbox "*Check* here if the data are unmerged but already scaled, ..."
must be checked.

Cheers

-- Ian


On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) <
graeme.win...@diamond.ac.uk> wrote:

> Dear  Dave, Star Aniso Developers,
>
> If this turns out to be because we are “missing something” i.e. there is
> an expectation on a property being present in the output files but it’s not
> there in our MTZ output, please let us know :-)
>
> Best wishes Graeme
>
> On 14 Jan 2020, at 09:06, David Lawson (JIC) 
> wrote:
>
> Dear ccp4bb
>
> I am trying to get the staraniso server to accept a scaled but unmerged
> mtz file from DIALS processing, but it reports an “Internal Server Error”
> after thinking about it for a while. Should this be possible? The file is
> 31 MB, so not huge.
>
> It works fine for a merged mtz from DIALS, but this is not the preferred
> option and I don’t get the full statistics I need for Table 1.
>
> Thanks in advance
>
> Dave Lawson
>
> ---
>
> Prof. David M. Lawson
> Department of Biological Chemistry,
> John Innes Centre,
> Norwich,
> NR4 7UH, UK.
> Tel: +44-(0)1603-450725
> Web: https://www.jic.ac.uk/people/david-lawson
> Email: david.law...@jic.ac.uk
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
>
> --
>
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
> --
>
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>



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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[David Waterman]

Hi Eleanor,

MTZ history is still useful, so from a recent xia2 run I can see (with
mtzdmp):

 * HISTORY for current MTZ file :

 From DIALS 2.0.1-gb22bab67b-release, run on 2019-11-21 at 10:59:17 GMT

It isn't possible to tell that the data were actually scaled in DIALS too
though, apart from the lack of POINTLESS and AIMLESS lines within the
history. As Graeme says, I think there are opportunities here for more
sophisticated tracking of provenance - certainly going back as far as
telling us where and when the images were collected would be most useful.

Cheers
-- David


On Tue, 14 Jan 2020 at 11:04, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> Not quite relevent but is there some way of stamping these files with a
> record of where they were generated ?
> I used to use my ability to read - name them myself as
> SAMPLEX-dialsprocessing-unmerged.mtz then
> SAMPLEX-dialsprocessing-unmerged-staranisod.mtz
>
> and there is an mtz feature which wrote a history with dates as well but
> now with automated file naming it is hard to keep track of how a file was
> generated.
>
>
> It seems likely that lots of Table !s do not describe the data set that
> was actually used for structure solution and deposition!
>
> Eleanor
>
> On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) <
> graeme.win...@diamond.ac.uk> wrote:
>
>> Dear  Dave, Star Aniso Developers,
>>
>> If this turns out to be because we are “missing something” i.e. there is
>> an expectation on a property being present in the output files but it’s not
>> there in our MTZ output, please let us know :-)
>>
>> Best wishes Graeme
>>
>> On 14 Jan 2020, at 09:06, David Lawson (JIC) 
>> wrote:
>>
>> Dear ccp4bb
>>
>> I am trying to get the staraniso server to accept a scaled but unmerged
>> mtz file from DIALS processing, but it reports an “Internal Server Error”
>> after thinking about it for a while. Should this be possible? The file is
>> 31 MB, so not huge.
>>
>> It works fine for a merged mtz from DIALS, but this is not the preferred
>> option and I don’t get the full statistics I need for Table 1.
>>
>> Thanks in advance
>>
>> Dave Lawson
>>
>> ---
>>
>> Prof. David M. Lawson
>> Department of Biological Chemistry,
>> John Innes Centre,
>> Norwich,
>> NR4 7UH, UK.
>> Tel: +44-(0)1603-450725
>> Web: https://www.jic.ac.uk/people/david-lawson
>> Email: david.law...@jic.ac.uk
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>>
>>
>>
>> --
>>
>> This e-mail and any attachments may contain confidential, copyright and
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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Hello Eleanor

Is that the sound of worms escaping a pot I hear in the distance? Certainly is!

Yes, this is something which was raised with a few of my colleagues at the 
study weekend and something we are discussing internally - with my facility hat 
on I think we should get to the bottom of this one - early in the year.

best wishes Graeme

On 14 Jan 2020, at 11:03, Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:

Not quite relevent but is there some way of stamping these files with a record 
of where they were generated ?
I used to use my ability to read - name them myself as
SAMPLEX-dialsprocessing-unmerged.mtz then
SAMPLEX-dialsprocessing-unmerged-staranisod.mtz

and there is an mtz feature which wrote a history with dates as well but now 
with automated file naming it is hard to keep track of how a file was generated.


It seems likely that lots of Table !s do not describe the data set that was 
actually used for structure solution and deposition!

Eleanor

On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) 
mailto:graeme.win...@diamond.ac.uk>> wrote:
Dear  Dave, Star Aniso Developers,

If this turns out to be because we are “missing something” i.e. there is an 
expectation on a property being present in the output files but it’s not there 
in our MTZ output, please let us know :-)

Best wishes Graeme

On 14 Jan 2020, at 09:06, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:

Dear ccp4bb

I am trying to get the staraniso server to accept a scaled but unmerged mtz 
file from DIALS processing, but it reports an “Internal Server Error” after 
thinking about it for a while. Should this be possible? The file is 31 MB, so 
not huge.

It works fine for a merged mtz from DIALS, but this is not the preferred option 
and I don’t get the full statistics I need for Table 1.

Thanks in advance

Dave Lawson

---

Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk




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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[Eleanor Dodson]

Not quite relevent but is there some way of stamping these files with a
record of where they were generated ?
I used to use my ability to read - name them myself as
SAMPLEX-dialsprocessing-unmerged.mtz then
SAMPLEX-dialsprocessing-unmerged-staranisod.mtz

and there is an mtz feature which wrote a history with dates as well but
now with automated file naming it is hard to keep track of how a file was
generated.


It seems likely that lots of Table !s do not describe the data set that was
actually used for structure solution and deposition!

Eleanor

On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) <
graeme.win...@diamond.ac.uk> wrote:

> Dear  Dave, Star Aniso Developers,
>
> If this turns out to be because we are “missing something” i.e. there is
> an expectation on a property being present in the output files but it’s not
> there in our MTZ output, please let us know :-)
>
> Best wishes Graeme
>
> On 14 Jan 2020, at 09:06, David Lawson (JIC) 
> wrote:
>
> Dear ccp4bb
>
> I am trying to get the staraniso server to accept a scaled but unmerged
> mtz file from DIALS processing, but it reports an “Internal Server Error”
> after thinking about it for a while. Should this be possible? The file is
> 31 MB, so not huge.
>
> It works fine for a merged mtz from DIALS, but this is not the preferred
> option and I don’t get the full statistics I need for Table 1.
>
> Thanks in advance
>
> Dave Lawson
>
> ---
>
> Prof. David M. Lawson
> Department of Biological Chemistry,
> John Innes Centre,
> Norwich,
> NR4 7UH, UK.
> Tel: +44-(0)1603-450725
> Web: https://www.jic.ac.uk/people/david-lawson
> Email: david.law...@jic.ac.uk
>
>
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>
> To unsubscribe from the CCP4BB list, click the following link:
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>
>
>
>
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> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
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[ccp4bb] Postdoctoral fellowship (2 years) to study membrane protein transport at Umeå University, Sweden

[Magnus Andersson]

The Andersson lab at the department of Chemistry at Umeå University, Sweden, is 
looking to recruit a postdoctoral fellow (2-year fellowship, funded by the 
Kempe foundation) to study membrane protein transport. The Andersson lab 
combines time-resolved X-ray solution scattering and computer simulations to 
determine membrane protein dynamics and transport in the lipid environment. The 
overall goals are to determine structures and timing of transient protein 
states in the membrane.
The research spans molecular biology production, nanodisc insertion, and 
characterization of proteins to development work at synchrotrons MAX IV (Lund) 
and ESRF (Grenoble). The project can also involve computer simulation – the 
extent to which will depend upon the background/interest of the Fellow. The 
work will be performed within the context of Integrated Structural Biology 
(https://www.biostruct.umu.se) at Umeå 
University that provides seminar series as well as an exciting research 
environment.
Qualifications
The required qualification is a doctoral degree in chemistry, biophysics, 
biochemistry, physics, or a foreign degree that is deemed equivalent. The 
applicant must have practical experience and expertise from protein production 
and characterization. Prior experience from working with membrane proteins, 
nanodisc insertion, structural biology, and computer simulations are considered 
merits. Good knowledge of the English language, both written and spoken, is 
required. A suitable candidate should also be creative, have good collaboration 
skills, a high degree of independence and problem-solving analytical ability.
 Application
The application should include:
- A cover letter stating why you want to join the lab and study membrane 
protein transport & dynamics (maximum 1 pages). This letter must also contain 
your contact details.
- A Curriculum Vitae including a list of peer-reviewed published articles
- Copies of doctoral degree certificate and other relevant degree certificates
- Name and contact information for two reference persons of which one should be 
your PhD supervisor
Send your complete application to: 
magnus.p.anders...@umu.se
Webpage: https://www.biostruct.umu.se/principal-investigators/magnus-andersson/


#
Magnus Andersson, Associate Professor
Integrated Structural Biology
Department of Chemistry
Umeå University

Email: magnus.p.anders...@umu.se
Phone: +46 720 837370

Mailing address:
Umeå University
Department of Chemistry
KBC-building
SE-901 87 Umeå

Visiting address:
Linnaeusvägen 6




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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear  Dave, Star Aniso Developers,

If this turns out to be because we are “missing something” i.e. there is an 
expectation on a property being present in the output files but it’s not there 
in our MTZ output, please let us know :-)

Best wishes Graeme

On 14 Jan 2020, at 09:06, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:

Dear ccp4bb

I am trying to get the staraniso server to accept a scaled but unmerged mtz 
file from DIALS processing, but it reports an “Internal Server Error” after 
thinking about it for a while. Should this be possible? The file is 31 MB, so 
not huge.

It works fine for a merged mtz from DIALS, but this is not the preferred option 
and I don’t get the full statistics I need for Table 1.

Thanks in advance

Dave Lawson

---

Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk




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privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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[ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[David Lawson (JIC)]

Dear ccp4bb

I am trying to get the staraniso server to accept a scaled but unmerged mtz 
file from DIALS processing, but it reports an "Internal Server Error" after 
thinking about it for a while. Should this be possible? The file is 31 MB, so 
not huge.

It works fine for a merged mtz from DIALS, but this is not the preferred option 
and I don't get the full statistics I need for Table 1.

Thanks in advance

Dave Lawson

---

Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk




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