[ccp4bb] Faculty position in The School of Pharmaceutical Sciences at Xiamen University

[苏迎]

Dear all,

Please note the following opening :

The School of Pharmaceutical Sciences at Xiamen University, China is seeking a 
highly motivated and talented protein crystallographer to join the faculty 
team.  Job position will be commensurate with the candidate's qualifications. 
(http://pharm.xmu.edu.cn/03/77/c7538a131959/page.htm) 

Qualifications include, but are not limited to:

•A Ph.D. in structural biology or a closely related discipline 

•Extensive experience in expressing and purifying protein from insect 
cell/baculovirus systems 

•Extensive experience in protein crystallography

•Experience with biophysical techniques such as SPR, CD and ITC

•Ability to work independently and collaboratively

•Good track record of publications

Application materials should be submitted to yin...@xmu.edu.cn. The application 
must include a cover letter, curriculum vitae, summary of research 
accomplishments, a  plan for future research, and names and contact information 
of three references. 

[ccp4bb] Postdoctoral Research Associate in molecular/structural biology

[O'Neill, Hugh Michael]

Postdoctoral Research Associate: Molecular / Structural Biologist
NB50594128

Direct Application Link:  
https://recruiting.ornl.gov/sap/bc/webdynpro/sap/hrrcf_a_posting_apply?sap-language=EN_INST_GUID=005056B439771ED6AB8C12A5EC79B451#
Also:  http://neutrons.ornl.gov/careers
The Neutron Sciences Directorate (NScD) at Oak Ridge National Laboratory (ORNL) 
operates the High Flux Isotope Reactor (HFIR), the United States' highest flux 
reactor based neutron source, and the Spallation Neutron Source (SNS), the 
world's most intense pulsed accelerator based neutron source. Together these 
facilities operate 30 instruments for neutron scattering research, each year 
carrying out in excess of 1,000 experiments in the physical, chemical, 
materials, biological and medical sciences. HFIR also provides unique 
facilities for isotope production and neutron irradiation. To learn more about 
Neutron Sciences at ORNL go to: http://neutrons.ornl.gov.
Purpose:
The Biology and Soft Matter Division at Oak Ridge National Laboratory (ORNL) 
invites applications for a post-doctoral molecular biologist or structural 
biologist to join its Energy and the Environment group. The successful 
candidate will join a multi-disciplinary research team investigating the 
structure and function of biological complexes that are involved in, for 
example, cellulose synthesis, biomass deconstruction and cell-signaling. These 
projects involve multi-task efforts in molecular biology, protein 
crystallography, small-angle scattering and computational modeling. The 
position represents an excellent opportunity for researchers to develop their 
careers and interact with leading scientists from around the world.  As an ORNL 
postdoctoral fellow you will have access to leading small angle scattering and 
neutron diffraction facilities, bio-fermentation laboratories, and biophysical 
characterization laboratories, in addition to in-house small angle X-ray 
scattering and X-ray diffraction instrumentation. The position represents an 
excellent opportunity for researchers to develop their careers and interact 
with leading scientists from around the world.

Major Duties/Responsibilities:
*Responsible for protein production, protein labeling, purification, 
development of novel labeling strategies
*Assist in protein crystallography and small-angle scattering studies
*Publish scientific papers on this collaborative research
*Present scientific results at appropriate national and international 
conferences
*Ensure compliance with environment, safety, health and quality program 
requirements
*Maintain strong commitment to the implementation and perpetuation of values 
and ethics
*Physical requirements for this job include the use of hand and eye protection 
gear, kneeling, sitting for extended periods of time, and extensive work at 
chemistry and biochemistry laboratories

Qualifications Required:

A Ph.D. degree in protein chemistry, biophysics or structural biology is 
required. The candidates should have a proven track record in molecular biology 
techniques including cloning, protein expression and purification, and in 
biophysical characterization using NMR/EPR or X-ray techniques.  The candidate 
should be self-motivated, have excellent interpersonal, communication and 
presentational skills and a demonstrated ability to interact effectively with 
staff at all levels within a multi-disciplinary team.



Applicants must have received their PhD within five years of this application 
and must complete all degree requirements before starting their appointment.



Employment is contingent upon the results of a pre-employment drug screen which 
must be administered and cleared before employment can begin.

Qualifications Desired:

Additional experience in expression and production of membrane proteins, 
eukaryotic expression systems, and cell-free protein synthesis would be a 
distinct advantage.

ORNL Benefits:
Oak Ridge National Laboratory offers an exceptional benefits package to include 
relocation, 401K, Paid Vacation and medical / dental plan.  Onsite amenities 
include Credit Union, Medical Clinic and free fitness facilities.

We accept Word(.doc, .docx), Excel(.xls, .xlsx), PowerPoint(.ppt, .pptx), 
Adobe(.pdf), Rich Text Format(.rtf), HTML(.htm, .hmtl) and text files(.txt) up 
to 2MB in size.

If you have trouble applying for a position, please email 
ornlrecruit...@ornl.gov.

ORNL is an equal opportunity employer. All qualified applicants, including 
individuals with disabilities and protected
veterans, are encouraged to apply. UT-Battelle is an E-Verify Employer.

[ccp4bb] Position posting at SBGrid/Harvard Medical School

[Michelle Ottaviano]

Title: Bioinformatics Software Specialist II

Harvard Medical School, Department of Biological Chemistry and Molecular
Pharmacology

Job summary:

The SBGrid Consortium at Harvard Medical School (www.sbgrid.org) is an
international collaboration to provide the biomedical community with
support for research computing. SBGrid’s primary service is the curation,
deployment, and maintenance of a comprehensive set of software and
computational tools that are useful in biomedical research. The SBGrid
software library is, effectively, a kind of scientific ‘app store’ that
allows users to access a wide range of up-to-date applications without
having to download, compile, configure, maintain, or update software. We
support over 300 different scientific applications and software suites on
Linux and OS X operating systems. Read more about the SBGrid project in our
eLife paper:  (https://elife.elifesciences.org/content/2/e01456
).

Primary job responsibilities:

The SBGrid Consortium has an immediate opening for a PhD level
Bioinformatics Software Specialist. The primary responsibilities of the
position will be installation, configuration, and testing of biomedical
software on Linux and OS X platforms for use in the Consortium laboratories
and providing bioinformatics software support for scientists at Harvard and
SBGrid institutions. Additional responsibilities include working with
scientific software developers to integrate new applications into the
software collection.

The scientific software in SBGrid’s collection is written in a polyglot of
languages (Fortran, C, C++, Python, Java, Perl, Tcl/Tk and sh/csh scripts)
and built with any one of a number of different build systems (autotools,
cmake, scons, homebrew shell scripts/makefiles, setuptools, etc). This
Bioinformatics Software Specialist position is a hybrid, in which some
software development experience is useful, but it is not a traditional
developer job in any sense. You will work in a multidisciplinary research
and computing environment that integrates cutting edge science, rapidly
evolving software workflows, high-performance computing, and novel data
collection instruments.

Qualifications:

   -

   Familiarity with bioinformatics and/or structural biology applications
   and workflows
   -

   Strong knowledge of Linux and OS X operating systems
   -

   Bash and/or csh shell scripting experience
   -

   Working knowledge of at least one programming language
   -

   Experience compiling and installing software from source and
   troubleshooting associated problems
   -

   Proficiency working in High-Performance Computing environments
   -

   Autodidact with strong attention to detail and enthusiasm for hard
   problems


Requirements:

PhD/MS in structural biology or bioinformatics.

Additional Qualifications:

The successful candidate will have excellent organizational skills and an
ability to work independently and prioritize work. Proven project and/or
program management skills. Excellent interpersonal and communications
skills.
To apply, email the SBGrid Consortium at ap...@hkl.hms.harvard.edu.

[ccp4bb] Antw: Re: [ccp4bb] R/Rfree values

[Matthias Barone]

Dear Rohit
Additionally to the very good suggestions, I'd feed the structure into
the PDB_REDO server. Its a fast and easy way to detect if the refinement
strategy is correct. The server gives you a good feeling how tight the
x-ray weights need to be. 
If however PDB_REDO does not manage to decrease the Rfactor gap of 7%, I
would suggest to switch to Phenix and give it a try.
If this does bring the factors down and relax the structure, let
pointless have a look into the XDS_ASCII file. Pointless and Xtriage are
two fast programs to detect if you are correct with the choice of the
space group. They give you also a first hint about twinning and the
amount of twinning.
good luck,
matthias




>>> Prem Prakash  14.12.16 19.20 Uhr >>>
Dear Rohit, I am totally agree with Mark, that just R free and R work
does not decide the structure solved, you have to see other parameters
as Mark already suggested. What is and redundancy and also what is the
mosaicity? please look at these parameters too. 

Best 
Prem 


On Wed, Dec 14, 2016 at 10:07 PM, Ashok Nayak 
wrote:
Dear Rohit,
Look at what percentage of the reflections are in the Rfree set, if its
less say 5 %; and you have a good redundancy you can use 10 %. You might
like to use the other Rfree set[1 if you have already used the 0 set] or
consider using the whole set of reflections as a free set if need be if
you suspect a bias in your Rfree set.
As suggested earlier I would also look at how the Fobs and Fcalc
correlate as a function of resolution from the sigma A plot or CC*
values.

Sometimes overestimating the resolution would add up more noise and it
would give you bad R values.

and If the molecule is elongated you might have diffraction anisotropy
and in that case The R values don't come down.

I would also like to use Refmac along with Phenix; that helped in my
case.

So you would like to take them one by one and figure out carefully.

Best Wishes

Ashok Nayak
Post-Doctoral Fellow,
Department of Physiology and Biophysics
VCU Medical Centre,1101 E Marshall ST, 
Richmond,VA
USA


  


On Wed, Dec 14, 2016 at 11:12 AM, Morais, Marc C. 
wrote:
  In addition to what others have mentioned, you might want to consider
the unpleasant possibility that part of your structure is simply built
incorrectly. Sometimes rebuilding a  short loop or even a few residues
in that loop can do the trick. Look carefully for regions of your map
with poor density and/or regions of your model with poor geometry, and
see if there might be an alternate way to build that region. There is
often a psychological  barrier to attempting these rebuilds, because
they are difficult (if they weren't we would have built correctly the
first time). However, once begun, it is often less painful than
expected. SA/composite omit maps can help.
   From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
Eleanor Dodson [eleanor.dod...@york.ac.uk]
 Sent: Wednesday, December 14, 2016 9:49 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] R/Rfree values
 
 
 
 es - look carefully at your data quality indicators - batch scales,
Wilson plot - moments etc.. tHese can show up if there is a problem with
ice rings or crystal decay or whatever. 
 
 Then I always look at the REFMAC plot of  v  
 
 If they overlap well - good - but problems with scaling will show up
there.
 
 
 Eleanor
 
 
 On 14 December 2016 at 15:21, Mark J van Raaij 
 wrote:
  Dear Rohit,
 
 I wouldn’t judge a structure just by the Rwork and Rfree values, but
also by the validation and other statistics (bond lengths, angles,
Ramachandran plot, map quality, fit to map, average B values). If these
are all ok, you should be able to “get away with”  an Rfree of 33%.
 In your email you state that you have already made a significant effort
in different refinement strategies, so perhaps there is no improvement
to be made there.
 The reason for good, and reprocessing might help. Although the most likely 
outcome is
that you can’t significantly improve it, but at least trying will put
your mind more at ease.
 In the end, the only way to improve the structure, and R-factors, may
be to grow a better crystal, cryo-protect better and/or collect better
data - this particular crystal may just have some kind of disorder.
 
 Greetings,
 
 Mark J van Raaij
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 calle Darwin 3
 E-28049 Madrid, Spain
 tel.  (+34) 91 585 4616
 http://wwwuser.cnb.csic.es/~mjvanraaij
  
 


 
 
 
 > On 14 Dec 2016, at 16:02, rohit kumar  wrote:
 >
 > Dear All,
 >
 > I am solving a data of 2.5 A (C121 space group). Right now the
R/Rfree values are 26/33, after many cycles of refinements (With or With
out water) the R/Rfree values still same. Zanuda suggests that the space
group seems to be correct and the model is looking  fine in coot.
 > Some one suggest what is the main problem.
 > Should I 

Re: [ccp4bb] R/Rfree values

[Sudipta Bhattacharyya]

Hi Rohit,

Along with many excellent suggestions you already got...I want to add the
possibility of the presence of  twining (even a small but significant
percent) and/or the presence of t-NCS in the data.

Good luck!
Sudipta.

On Wed, Dec 14, 2016 at 12:19 PM, Prem Prakash  wrote:

> Dear Rohit,
> I am totally agree with Mark, that just R free and R work does not decide
> the structure solved, you have to see other parameters as Mark already
> suggested. What is and redundancy and also what is the mosaicity? please
> look at these parameters too.
>
> Best
> Prem
>
> On Wed, Dec 14, 2016 at 10:07 PM, Ashok Nayak 
> wrote:
>
>> Dear Rohit,
>>
>> Look at what percentage of the reflections are in the Rfree set, if its
>> less say 5 %; and you have a good redundancy you can use 10 %. You might
>> like to use the other Rfree set[1 if you have already used the 0 set] or
>> consider using the whole set of reflections as a free set if need be if you
>> suspect a bias in your Rfree set.
>>
>> As suggested earlier I would also look at how the Fobs and Fcalc
>> correlate as a function of resolution from the sigma A plot or CC* values.
>>
>> Sometimes overestimating the resolution would add up more noise and it
>> would give you bad R values.
>>
>> and If the molecule is elongated you might have diffraction anisotropy
>> and in that case The R values don't come down.
>>
>> I would also like to use Refmac along with Phenix; that helped in my case.
>>
>> So you would like to take them one by one and figure out carefully.
>>
>> Best Wishes
>>
>> Ashok Nayak
>> Post-Doctoral Fellow,
>> Department of Physiology and Biophysics
>> VCU Medical Centre,1101 E Marshall ST,
>> Richmond,VA
>> USA
>>
>>
>>
>> On Wed, Dec 14, 2016 at 11:12 AM, Morais, Marc C. 
>> wrote:
>>
>>> In addition to what others have mentioned, you might want to consider
>>> the unpleasant possibility that part of your structure is simply built
>>> incorrectly. Sometimes rebuilding a short loop or even a few residues in
>>> that loop can do the trick. Look carefully for regions of your map with
>>> poor density and/or regions of your model with poor geometry, and see if
>>> there might be an alternate way to build that region. There is often a
>>> psychological barrier to attempting these rebuilds, because they are
>>> difficult (if they weren't we would have built correctly the first time).
>>> However, once begun, it is often less painful than expected. SA/composite
>>> omit maps can help.
>>> --
>>> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
>>> Eleanor Dodson [eleanor.dod...@york.ac.uk]
>>> *Sent:* Wednesday, December 14, 2016 9:49 AM
>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>> *Subject:* Re: [ccp4bb] R/Rfree values
>>>
>>> es - look carefully at your data quality indicators - batch scales,
>>> Wilson plot - moments etc.. tHese can show up if there is a problem with
>>> ice rings or crystal decay or whatever.
>>> Then I always look at the REFMAC plot of  v 
>>> If they overlap well - good - but problems with scaling will show up
>>> there.
>>>
>>> Eleanor
>>>
>>> On 14 December 2016 at 15:21, Mark J van Raaij 
>>> wrote:
>>>
 Dear Rohit,

 I wouldn’t judge a structure just by the Rwork and Rfree values, but
 also by the validation and other statistics (bond lengths, angles,
 Ramachandran plot, map quality, fit to map, average B values). If these are
 all ok, you should be able to “get away with” an Rfree of 33%.
 In your email you state that you have already made a significant effort
 in different refinement strategies, so perhaps there is no improvement to
 be made there.
 The reason for the high-ish Rfree could be that the data is not so
 good, and reprocessing might help. Although the most likely outcome is that
 you can’t significantly improve it, but at least trying will put your mind
 more at ease.
 In the end, the only way to improve the structure, and R-factors, may
 be to grow a better crystal, cryo-protect better and/or collect better data
 - this particular crystal may just have some kind of disorder.

 Greetings,

 Mark J van Raaij
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 calle Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://wwwuser.cnb.csic.es/~mjvanraaij







 > On 14 Dec 2016, at 16:02, rohit kumar  wrote:
 >
 > Dear All,
 >
 > I am solving a data of 2.5 A (C121 space group). Right now the
 R/Rfree values are 26/33, after many cycles of refinements (With or With
 out water) the R/Rfree values still same. Zanuda suggests that the space
 group seems to be correct and the model is looking fine in coot.
 > Some one suggest what is the main problem.
 > Should I again 

Re: [ccp4bb] R/Rfree values

[Prem Prakash]

Dear Rohit,
I am totally agree with Mark, that just R free and R work does not decide
the structure solved, you have to see other parameters as Mark already
suggested. What is and redundancy and also what is the mosaicity? please
look at these parameters too.

Best
Prem

On Wed, Dec 14, 2016 at 10:07 PM, Ashok Nayak 
wrote:

> Dear Rohit,
>
> Look at what percentage of the reflections are in the Rfree set, if its
> less say 5 %; and you have a good redundancy you can use 10 %. You might
> like to use the other Rfree set[1 if you have already used the 0 set] or
> consider using the whole set of reflections as a free set if need be if you
> suspect a bias in your Rfree set.
>
> As suggested earlier I would also look at how the Fobs and Fcalc correlate
> as a function of resolution from the sigma A plot or CC* values.
>
> Sometimes overestimating the resolution would add up more noise and it
> would give you bad R values.
>
> and If the molecule is elongated you might have diffraction anisotropy and
> in that case The R values don't come down.
>
> I would also like to use Refmac along with Phenix; that helped in my case.
>
> So you would like to take them one by one and figure out carefully.
>
> Best Wishes
>
> Ashok Nayak
> Post-Doctoral Fellow,
> Department of Physiology and Biophysics
> VCU Medical Centre,1101 E Marshall ST,
> Richmond,VA
> USA
>
>
>
> On Wed, Dec 14, 2016 at 11:12 AM, Morais, Marc C. 
> wrote:
>
>> In addition to what others have mentioned, you might want to consider the
>> unpleasant possibility that part of your structure is simply built
>> incorrectly. Sometimes rebuilding a short loop or even a few residues in
>> that loop can do the trick. Look carefully for regions of your map with
>> poor density and/or regions of your model with poor geometry, and see if
>> there might be an alternate way to build that region. There is often a
>> psychological barrier to attempting these rebuilds, because they are
>> difficult (if they weren't we would have built correctly the first time).
>> However, once begun, it is often less painful than expected. SA/composite
>> omit maps can help.
>> --
>> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor
>> Dodson [eleanor.dod...@york.ac.uk]
>> *Sent:* Wednesday, December 14, 2016 9:49 AM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] R/Rfree values
>>
>> es - look carefully at your data quality indicators - batch scales,
>> Wilson plot - moments etc.. tHese can show up if there is a problem with
>> ice rings or crystal decay or whatever.
>> Then I always look at the REFMAC plot of  v 
>> If they overlap well - good - but problems with scaling will show up
>> there.
>>
>> Eleanor
>>
>> On 14 December 2016 at 15:21, Mark J van Raaij 
>> wrote:
>>
>>> Dear Rohit,
>>>
>>> I wouldn’t judge a structure just by the Rwork and Rfree values, but
>>> also by the validation and other statistics (bond lengths, angles,
>>> Ramachandran plot, map quality, fit to map, average B values). If these are
>>> all ok, you should be able to “get away with” an Rfree of 33%.
>>> In your email you state that you have already made a significant effort
>>> in different refinement strategies, so perhaps there is no improvement to
>>> be made there.
>>> The reason for the high-ish Rfree could be that the data is not so good,
>>> and reprocessing might help. Although the most likely outcome is that you
>>> can’t significantly improve it, but at least trying will put your mind more
>>> at ease.
>>> In the end, the only way to improve the structure, and R-factors, may be
>>> to grow a better crystal, cryo-protect better and/or collect better data -
>>> this particular crystal may just have some kind of disorder.
>>>
>>> Greetings,
>>>
>>> Mark J van Raaij
>>> Dpto de Estructura de Macromoleculas
>>> Centro Nacional de Biotecnologia - CSIC
>>> calle Darwin 3
>>> E-28049 Madrid, Spain
>>> tel. (+34) 91 585 4616
>>> http://wwwuser.cnb.csic.es/~mjvanraaij
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> > On 14 Dec 2016, at 16:02, rohit kumar  wrote:
>>> >
>>> > Dear All,
>>> >
>>> > I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree
>>> values are 26/33, after many cycles of refinements (With or With out water)
>>> the R/Rfree values still same. Zanuda suggests that the space group seems
>>> to be correct and the model is looking fine in coot.
>>> > Some one suggest what is the main problem.
>>> > Should I again process my data? And what is the best way to fine right
>>> space group (If problem with space group).
>>> > Please tell me if you need any information regarding may data.
>>> >
>>> > --
>>> > WITH REGARDS
>>> > Rohit Kumar Singh
>>> > Lab. no. 430,
>>> > P.I. Dr. S. Gourinath,
>>> > School of Life Sciences,
>>> > Jawaharlal Nehru University
>>> > New Delhi -110067
>>>
>>
>>
>
>
> --
>
>

Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

[Bernhard Rupp (Hofkristallrat a.D.)]

The replacement of the EDS might be an excellent opportunity to
upgrade/include the newer EDSTATS metrics and
make these raw data also downloadable/parse-able for analysis purposes
(xml). 
A server option where you can send in your own PDB files (included in the
validation server?) before submission might 
be useful (the current ccp4 implementation of EDSTATS fails to
convince)...the effect of the deterrence experiencing
public maps/stats looking as bad as the ones dreamt up at home might enhance
deposition quality.

Best, BR  

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard
DVD Kleywegt
Sent: Tuesday, December 13, 2016 9:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

Hi all,

After tirelessly serving the scientific community with (mostly) beautiful
maps for two decades, the Uppsala Electron Density Server (EDS;
http://eds.bmc.uu.se/) is now reaching the end of its life (in fact, it has
been living on borrowed time for several years already). Some time in 2017
it will therefore be "phased" out and join the choir invisible (despite its
beautiful plumage).

The good news is that much of the EDS functionality (and in particular the
delivery of map and mtz files, as well as a much better 3D viewer) is now
provided by the Protein Data Bank in Europe (PDBe; http://pdbe.org/).

There is a short write-up that explains what this means for users who just
want to look at maps, for users who want to download files, for users of
software that retrieves data from EDS, and for developers of such software
(incl. URLs for map, mtz and other relevant files on the PDBe website) at:

   http://www.ebi.ac.uk/pdbe/eds

Toodle pip!

--Gerard

**
Gerard J. Kleywegt

   http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
The opinions in this message are fictional.  Any similarity
to actual opinions, living or dead, is purely coincidental.
**
Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
 of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] Bug in latest COOT

[Olga Moroz]

Same with me, I have Mac OS 10.11.6 (El CApitan).
I couldn’t add terminal residues, then went three CCP4 updates back, it got OK,
but I still can’t add OXT.

Olga




> On 14 Dec 2016, at 04:51, Jobichen Chacko  wrote:
> 
> Dear All,
> Any solution to this problem.
> I am also encountering this issue with MacOS, managed to revert back
> from the latest CCP4 update and it is working fine.
> Thanks.
> Jobi
> 
> On Sat, Dec 10, 2016 at 2:42 AM, David Waterman  wrote:
>> Dear Oliver,
>> 
>> Thanks for digging deeper. I don't know why this should matter either, but
>> now we should be able to investigate further.
>> 
>> Cheers
>> David
>> 
>> 
>> On Fri, 9 Dec 2016, 18:03 "Weiergräber, Oliver H.",
>>  wrote:
>>> 
>>> Dear David,
>>> 
>>> well, 1D2F does cause the issue for me, or at least it _did_ until I found
>>> the real issue.
>>> 
>>> In fact, I could not reproduce the problem on a second machine, so I
>>> started testing for problems with my user environment (by cleaning up my
>>> shell start-up file to the bare minimum, deleting .coot-preferences etc.),
>>> but to no avail.
>>> What finally turned out to be responsible was a tiny modification to the
>>> system-wide environment: I had recently added /usr/lib64/gtk-2.0/modules to
>>> the ld.so.conf path in order to expose these (default) libraries to
>>> third-party programs that would not otherwise find them. After removing this
>>> path, geometry analysis in coot started working again. But it's really hard
>>> to understand how these libraries should be harmful to the operation of
>>> coot, and specifically prevent it from properly handling OXT atoms.
>>> And all this did not affect Paul's version...
>>> 
>>> Anyway, thanks a lot for looking into this
>>> Oliver
>>> 
>>> 
>>>  PD Dr. Oliver H. Weiergräber
>>>  Institute of Complex Systems
>>>  ICS-6: Structural Biochemistry
>>>  Tel.: +49 2461 61-2028
>>>  Fax: +49 2461 61-9540
>>> 
>>> 
>>> 
>>> 
>>> 
>>> From: David Waterman [dgwater...@gmail.com]
>>> Sent: Friday, December 09, 2016 4:38 PM
>>> To: Weiergräber, Oliver H.
>>> Cc: CCP4BB@jiscmail.ac.uk
>>> Subject: Re: [ccp4bb] Bug in latest COOT
>>> 
>>> Dear Oliver,
>>> 
>>> I just tried this on 1D2F using computers at Diamond (Red Hat Enterprise
>>> Linux Workstation release 6.8 (Santiago)) with coot in CCP4 7.0.025 and all
>>> was well.
>>> 
>>> Could you send me, or point me towards, a PDB that causes the issue - and
>>> exact instructions for how to trigger it?
>>> 
>>> Cheers
>>> 
>>> -- David
>>> 
>>> On 9 December 2016 at 14:59, "Weiergräber, Oliver H."
>>> >
>>> wrote:
>>> Hello Paul and ccp4 devs,
>>> 
>>> as I mentioned, the crashing coot version is the one provided with the
>>> latest ccp4 update(s), i.e.
>>> 
>>> ---
>>> 0.8.7 (revision-count 6498)
>>> [with guile 1.8.8 embedded]
>>> [with python 2.7.10 embedded]
>>> Binary type: Linux-x86_64-centos-5-python-gtk2
>>> Builder_info: CCP4, Oxfordshire
>>> ---
>>> 
>>> Running CentOS 6.8 here, but any EL6 incarnation should behave in the same
>>> way.
>>> 
>>> This is the console output after invoking geometry analysis:
>>> ---
>>> Unknown element ::
>>> /usr/local/ccp4-7.0/bin/coot: line 284: 17416 Segmentation fault
>>> (core dumped) $coot_bin "$@"
>>> coot-exe: "/usr/local/ccp4-7.0/libexec/coot-bin"
>>> coot-version:
>>> /usr/local/ccp4-7.0/libexec/coot-bin
>>> platform:
>>> /bin/uname
>>> core: #f
>>> No core file found.  No debugging
>>> ---
>>> 
>>> Line 284 is just the final fi statement, without obvious (to me at least)
>>> relation to geometry analysis ...
>>> 
>>> Hope this helps
>>> Oliver
>>> 
>>> 
>>>  PD Dr. Oliver H. Weiergräber
>>>  Institute of Complex Systems
>>>  ICS-6: Structural Biochemistry
>>>  Tel.: +49 2461 61-2028
>>>  Fax: +49 2461 61-9540
>>> 
>>> 
>>> 
>>> 
>>> 
>>> From: CCP4 bulletin board
>>> [CCP4BB@JISCMAIL.AC.UK] on behalf of Paul
>>> Emsley [pems...@mrc-lmb.cam.ac.uk]
>>> Sent: Friday, December 09, 2016 3:31 PM
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Subject: Re: [ccp4bb] Bug in latest COOT
>>> 
>>> On 09/12/16 14:13, "Weiergräber, Oliver H." wrote:
 Hello,
 
 after installing the latest ccp4 updates today, I found that coot will
 consistently crash (core dump) if geometry analysis is run on _any_
 structure containing an OXT atom.
 
 
>>> 

[ccp4bb] 2016 Remediation of 3DEM Entries in the PDB archive

[Jasmine Young]

The wwPDB and the EMDataBank/Unified Data Resource for 3DEM Project 
 have collaborated to 
update the experimental methods descriptions of all electron microscopy 
and electron crystallography-derived structures in the PDB archive. With 
this work now completed, all 3DEM-derived entries have better-organized 
content and conform to the revised data model developed by the 
EMDataBank team for use within the wwPDB OneDep System 
. The OneDep System has 
supported deposition, annotation, and validation of 3DEM structures and 
fully integrates deposition of 3DEM maps and model coordinates since 
January 2016.


Examples of 3DEM model files (both remediated and from the OneDep 
system) are provided in a new wwPDB ftp directory 
(ftp://ftp.wwpdb.org/pub/pdb/test_data/EM/). A data-item level 
description of the changes made during remediation is provided here 
. 
3DEM terms in the updated PDBx/mmCIF dictionary can be reviewed here 
.


Files in the current PDB ftp archive will be replaced with new files 
corresponding to the updated PDBx/mmCIF dictionary in 2017. Users are 
encouraged to review and test the example data files.


We welcome your feedback. Please send any comments or questions to 
deposit-h...@mail.wwpdb.org.




--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

Re: [ccp4bb] R/Rfree values

[Ashok Nayak]

Dear Rohit,

Look at what percentage of the reflections are in the Rfree set, if its
less say 5 %; and you have a good redundancy you can use 10 %. You might
like to use the other Rfree set[1 if you have already used the 0 set] or
consider using the whole set of reflections as a free set if need be if you
suspect a bias in your Rfree set.

As suggested earlier I would also look at how the Fobs and Fcalc correlate
as a function of resolution from the sigma A plot or CC* values.

Sometimes overestimating the resolution would add up more noise and it
would give you bad R values.

and If the molecule is elongated you might have diffraction anisotropy and
in that case The R values don't come down.

I would also like to use Refmac along with Phenix; that helped in my case.

So you would like to take them one by one and figure out carefully.

Best Wishes

Ashok Nayak
Post-Doctoral Fellow,
Department of Physiology and Biophysics
VCU Medical Centre,1101 E Marshall ST,
Richmond,VA
USA



On Wed, Dec 14, 2016 at 11:12 AM, Morais, Marc C.  wrote:

> In addition to what others have mentioned, you might want to consider the
> unpleasant possibility that part of your structure is simply built
> incorrectly. Sometimes rebuilding a short loop or even a few residues in
> that loop can do the trick. Look carefully for regions of your map with
> poor density and/or regions of your model with poor geometry, and see if
> there might be an alternate way to build that region. There is often a
> psychological barrier to attempting these rebuilds, because they are
> difficult (if they weren't we would have built correctly the first time).
> However, once begun, it is often less painful than expected. SA/composite
> omit maps can help.
> --
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor
> Dodson [eleanor.dod...@york.ac.uk]
> *Sent:* Wednesday, December 14, 2016 9:49 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] R/Rfree values
>
> es - look carefully at your data quality indicators - batch scales, Wilson
> plot - moments etc.. tHese can show up if there is a problem with ice rings
> or crystal decay or whatever.
> Then I always look at the REFMAC plot of  v 
> If they overlap well - good - but problems with scaling will show up there.
>
> Eleanor
>
> On 14 December 2016 at 15:21, Mark J van Raaij 
> wrote:
>
>> Dear Rohit,
>>
>> I wouldn’t judge a structure just by the Rwork and Rfree values, but also
>> by the validation and other statistics (bond lengths, angles, Ramachandran
>> plot, map quality, fit to map, average B values). If these are all ok, you
>> should be able to “get away with” an Rfree of 33%.
>> In your email you state that you have already made a significant effort
>> in different refinement strategies, so perhaps there is no improvement to
>> be made there.
>> The reason for the high-ish Rfree could be that the data is not so good,
>> and reprocessing might help. Although the most likely outcome is that you
>> can’t significantly improve it, but at least trying will put your mind more
>> at ease.
>> In the end, the only way to improve the structure, and R-factors, may be
>> to grow a better crystal, cryo-protect better and/or collect better data -
>> this particular crystal may just have some kind of disorder.
>>
>> Greetings,
>>
>> Mark J van Raaij
>> Dpto de Estructura de Macromoleculas
>> Centro Nacional de Biotecnologia - CSIC
>> calle Darwin 3
>> E-28049 Madrid, Spain
>> tel. (+34) 91 585 4616
>> http://wwwuser.cnb.csic.es/~mjvanraaij
>>
>>
>>
>>
>>
>>
>>
>> > On 14 Dec 2016, at 16:02, rohit kumar  wrote:
>> >
>> > Dear All,
>> >
>> > I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree
>> values are 26/33, after many cycles of refinements (With or With out water)
>> the R/Rfree values still same. Zanuda suggests that the space group seems
>> to be correct and the model is looking fine in coot.
>> > Some one suggest what is the main problem.
>> > Should I again process my data? And what is the best way to fine right
>> space group (If problem with space group).
>> > Please tell me if you need any information regarding may data.
>> >
>> > --
>> > WITH REGARDS
>> > Rohit Kumar Singh
>> > Lab. no. 430,
>> > P.I. Dr. S. Gourinath,
>> > School of Life Sciences,
>> > Jawaharlal Nehru University
>> > New Delhi -110067
>>
>
>


--

Re: [ccp4bb] Why aren't green reflections on Mosflm integrated?

[zbyszek]

Walt is correct, the denzo/HKL2000 is an exception. It integrates all 
reflections that cross the Evald sphere, due to having special treatment 
of reflections with large Lorentz correction. It works fine in normal 
cases, even with somewhat misaligned rotation axis. These reflections 
are measured more precisely, although maybe somewhat less accurately.


Zbyszek Otwinowski



In 2016-12-14 04:07, Andrew Leslie wrote:

Dear Walt,

 As Tim has said, this is indeed related to the
Lorentz correction. These reflections have a large Lorentz correction
which is also very sensitive to the crystal orientation, so any small
error in orientation can result in a big change to the Lorentz
correction and thus to the corrected intensity. However, the default
maximum reflection width can be changed (Experiment settings, Advanced
Integration) and sometimes this is necessary to avoid excluding too
many reflections in cases where the mosaic spread is very high (> 1°
say) or the mosaic block size is small.

I think this feature is common to all integration programs, although
the default settings may well be different.

Best wishes,

Andrew
On 14 Dec 2016, at 01:40, Hank  wrote:


Dear CCP4BB users,

I have a question about Mosflm. The manual says green predictions have
"reflection width greater than 5 degrees" and will not be integrated. 
I always
assumed it should have something to do with Lorentz factor but not 
quite sure.
Why is it so? I'm not aware of such geometrical restriction in 
HKL2000.

Thank you!

Walt

Re: [ccp4bb] R/Rfree values

[Morais, Marc C.]

In addition to what others have mentioned, you might want to consider the 
unpleasant possibility that part of your structure is simply built incorrectly. 
Sometimes rebuilding a short loop or even a few residues in that loop can do 
the trick. Look carefully for regions of your map with poor density and/or 
regions of your model with poor geometry, and see if there might be an 
alternate way to build that region. There is often a psychological barrier to 
attempting these rebuilds, because they are difficult (if they weren't we would 
have built correctly the first time). However, once begun, it is often less 
painful than expected. SA/composite omit maps can help.

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson 
[eleanor.dod...@york.ac.uk]
Sent: Wednesday, December 14, 2016 9:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] R/Rfree values

es - look carefully at your data quality indicators - batch scales, Wilson plot 
- moments etc.. tHese can show up if there is a problem with ice rings or 
crystal decay or whatever.
Then I always look at the REFMAC plot of  v 
If they overlap well - good - but problems with scaling will show up there.

Eleanor

On 14 December 2016 at 15:21, Mark J van Raaij 
> wrote:
Dear Rohit,

I wouldn’t judge a structure just by the Rwork and Rfree values, but also by 
the validation and other statistics (bond lengths, angles, Ramachandran plot, 
map quality, fit to map, average B values). If these are all ok, you should be 
able to “get away with” an Rfree of 33%.
In your email you state that you have already made a significant effort in 
different refinement strategies, so perhaps there is no improvement to be made 
there.
The reason for the high-ish Rfree could be that the data is not so good, and 
reprocessing might help. Although the most likely outcome is that you can’t 
significantly improve it, but at least trying will put your mind more at ease.
In the end, the only way to improve the structure, and R-factors, may be to 
grow a better crystal, cryo-protect better and/or collect better data - this 
particular crystal may just have some kind of disorder.

Greetings,

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij







> On 14 Dec 2016, at 16:02, rohit kumar 
> > wrote:
>
> Dear All,
>
> I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree values 
> are 26/33, after many cycles of refinements (With or With out water) the 
> R/Rfree values still same. Zanuda suggests that the space group seems to be 
> correct and the model is looking fine in coot.
> Some one suggest what is the main problem.
> Should I again process my data? And what is the best way to fine right space 
> group (If problem with space group).
> Please tell me if you need any information regarding may data.
>
> --
> WITH REGARDS
> Rohit Kumar Singh
> Lab. no. 430,
> P.I. Dr. S. Gourinath,
> School of Life Sciences,
> Jawaharlal Nehru University
> New Delhi -110067

Re: [ccp4bb] R/Rfree values

[Eleanor Dodson]

es - look carefully at your data quality indicators - batch scales, Wilson
plot - moments etc.. tHese can show up if there is a problem with ice rings
or crystal decay or whatever.
Then I always look at the REFMAC plot of  v 
If they overlap well - good - but problems with scaling will show up there.

Eleanor

On 14 December 2016 at 15:21, Mark J van Raaij 
wrote:

> Dear Rohit,
>
> I wouldn’t judge a structure just by the Rwork and Rfree values, but also
> by the validation and other statistics (bond lengths, angles, Ramachandran
> plot, map quality, fit to map, average B values). If these are all ok, you
> should be able to “get away with” an Rfree of 33%.
> In your email you state that you have already made a significant effort in
> different refinement strategies, so perhaps there is no improvement to be
> made there.
> The reason for the high-ish Rfree could be that the data is not so good,
> and reprocessing might help. Although the most likely outcome is that you
> can’t significantly improve it, but at least trying will put your mind more
> at ease.
> In the end, the only way to improve the structure, and R-factors, may be
> to grow a better crystal, cryo-protect better and/or collect better data -
> this particular crystal may just have some kind of disorder.
>
> Greetings,
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
>
>
>
>
>
>
>
> > On 14 Dec 2016, at 16:02, rohit kumar  wrote:
> >
> > Dear All,
> >
> > I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree
> values are 26/33, after many cycles of refinements (With or With out water)
> the R/Rfree values still same. Zanuda suggests that the space group seems
> to be correct and the model is looking fine in coot.
> > Some one suggest what is the main problem.
> > Should I again process my data? And what is the best way to fine right
> space group (If problem with space group).
> > Please tell me if you need any information regarding may data.
> >
> > --
> > WITH REGARDS
> > Rohit Kumar Singh
> > Lab. no. 430,
> > P.I. Dr. S. Gourinath,
> > School of Life Sciences,
> > Jawaharlal Nehru University
> > New Delhi -110067
>

Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

[Eleanor Dodson]

Thank you Uppsala lot - it has been a great service and taught a lot of
people that "The map is the Message"
Eleanor Dodson

On 14 December 2016 at 12:54, Daniel Picot  wrote:

> Veni vidi
> I wil have to change my advices and lectures: go and look at the Uppsala
> Electron Density Server EDS
> It has been extremely useful.
> Even sometimes vici
> Daniel
>
>
>
>
> Le 13/12/2016 à 19:52, Patrick Loll a écrit :
>
>> Ave atque vale.
>>
>> The EDS was hugely useful (and will continue to be so in its new
>> manifestation, we hope)—thanks to everyone who made it happen!
>>
>> Pat
>>
>>
>>
>>> On 13 Dec 2016, at 12:51 PM, Gerard DVD Kleywegt 
>>> wrote:
>>>
>>> Hi all,
>>>
>>> After tirelessly serving the scientific community with (mostly)
>>> beautiful maps for two decades, the Uppsala Electron Density Server (EDS;
>>> http://eds.bmc.uu.se/) is now reaching the end of its life (in fact, it
>>> has been living on borrowed time for several years already). Some time in
>>> 2017 it will therefore be "phased" out and join the choir invisible
>>> (despite its beautiful plumage).
>>>
>>> The good news is that much of the EDS functionality (and in particular
>>> the delivery of map and mtz files, as well as a much better 3D viewer) is
>>> now provided by the Protein Data Bank in Europe (PDBe; http://pdbe.org/
>>> ).
>>>
>>> There is a short write-up that explains what this means for users who
>>> just want to look at maps, for users who want to download files, for users
>>> of software that retrieves data from EDS, and for developers of such
>>> software (incl. URLs for map, mtz and other relevant files on the PDBe
>>> website) at:
>>>
>>>   http://www.ebi.ac.uk/pdbe/eds
>>>
>>> Toodle pip!
>>>
>>> --Gerard
>>>
>>> **
>>>Gerard J. Kleywegt
>>>
>>>   http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
>>> **
>>>The opinions in this message are fictional.  Any similarity
>>>to actual opinions, living or dead, is purely coincidental.
>>> **
>>>Little known gastromathematical curiosity: let "z" be the
>>>radius and "a" the thickness of a pizza. Then the volume
>>> of that pizza is equal to pi*z*z*a !
>>> **
>>>
>>

Re: [ccp4bb] R/Rfree values

[Mark J van Raaij]

Dear Rohit,

I wouldn’t judge a structure just by the Rwork and Rfree values, but also by 
the validation and other statistics (bond lengths, angles, Ramachandran plot, 
map quality, fit to map, average B values). If these are all ok, you should be 
able to “get away with” an Rfree of 33%.
In your email you state that you have already made a significant effort in 
different refinement strategies, so perhaps there is no improvement to be made 
there.
The reason for the high-ish Rfree could be that the data is not so good, and 
reprocessing might help. Although the most likely outcome is that you can’t 
significantly improve it, but at least trying will put your mind more at ease.
In the end, the only way to improve the structure, and R-factors, may be to 
grow a better crystal, cryo-protect better and/or collect better data - this 
particular crystal may just have some kind of disorder.

Greetings,

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij







> On 14 Dec 2016, at 16:02, rohit kumar  wrote:
> 
> Dear All,
> 
> I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree values 
> are 26/33, after many cycles of refinements (With or With out water) the 
> R/Rfree values still same. Zanuda suggests that the space group seems to be 
> correct and the model is looking fine in coot. 
> Some one suggest what is the main problem.
> Should I again process my data? And what is the best way to fine right space 
> group (If problem with space group).
> Please tell me if you need any information regarding may data.  
> 
> -- 
> WITH REGARDS
> Rohit Kumar Singh
> Lab. no. 430,
> P.I. Dr. S. Gourinath,
> School of Life Sciences,
> Jawaharlal Nehru University
> New Delhi -110067

Re: [ccp4bb] R/Rfree values

[Rajesh Kumar]

Dear Rohit,

Try to run sfcheck or XTRIAGE and check, if your data is fine. Check for
twinning or pseudo-translation. You can send your processed mtz to me and I
would be more than happy to help you.

You can look into cumulative intensity distribution (if you processed with
XDS, it will be in CORRECT.LP file) and it will give you indication of
twinning.


Thank you
Rajesh

 ---x
With regards
Rajesh K. Harijan, Ph.D.
Albert Einstein College of Medicine
1300 Morris Park Ave., Bronx, NY 10461
Tel: 718.430.2777  |  Fax: 718.430.8565



On Wed, Dec 14, 2016 at 10:02 AM, rohit kumar  wrote:

> Dear All,
>
> I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree
> values are 26/33, after many cycles of refinements (With or With out water)
> the R/Rfree values still same. Zanuda suggests that the space group seems
> to be correct and the model is looking fine in coot.
> Some one suggest what is the main problem.
> Should I again process my data? And what is the best way to fine right
> space group (If problem with space group).
> Please tell me if you need any information regarding may data.
>
> --
> WITH REGARDS
> Rohit Kumar Singh
> Lab. no. 430,
> P.I. Dr. S. Gourinath,
> School of Life Sciences,
> Jawaharlal Nehru University
> New Delhi -110067
>

[ccp4bb] R/Rfree values

[rohit kumar]

Dear All,

I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree
values are 26/33, after many cycles of refinements (With or With out water)
the R/Rfree values still same. Zanuda suggests that the space group seems
to be correct and the model is looking fine in coot.
Some one suggest what is the main problem.
Should I again process my data? And what is the best way to fine right
space group (If problem with space group).
Please tell me if you need any information regarding may data.

-- 
WITH REGARDS
Rohit Kumar Singh
Lab. no. 430,
P.I. Dr. S. Gourinath,
School of Life Sciences,
Jawaharlal Nehru University
New Delhi -110067

Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

[Daniel Picot]

Veni vidi
I wil have to change my advices and lectures: go and look at the Uppsala 
Electron Density Server EDS

It has been extremely useful.
Even sometimes vici
Daniel



Le 13/12/2016 à 19:52, Patrick Loll a écrit :

Ave atque vale.

The EDS was hugely useful (and will continue to be so in its new manifestation, 
we hope)—thanks to everyone who made it happen!

Pat

  

On 13 Dec 2016, at 12:51 PM, Gerard DVD Kleywegt  wrote:

Hi all,

After tirelessly serving the scientific community with (mostly) beautiful maps for two 
decades, the Uppsala Electron Density Server (EDS; http://eds.bmc.uu.se/) is now reaching 
the end of its life (in fact, it has been living on borrowed time for several years 
already). Some time in 2017 it will therefore be "phased" out and join the 
choir invisible (despite its beautiful plumage).

The good news is that much of the EDS functionality (and in particular the 
delivery of map and mtz files, as well as a much better 3D viewer) is now 
provided by the Protein Data Bank in Europe (PDBe; http://pdbe.org/).

There is a short write-up that explains what this means for users who just want 
to look at maps, for users who want to download files, for users of software 
that retrieves data from EDS, and for developers of such software (incl. URLs 
for map, mtz and other relevant files on the PDBe website) at:

  http://www.ebi.ac.uk/pdbe/eds

Toodle pip!

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] Why aren't green reflections on Mosflm integrated?

[Andrew Leslie]

Dear Walt,

 As Tim has said, this is indeed related to the Lorentz 
correction. These reflections have a large Lorentz correction which is also 
very sensitive to the crystal orientation, so any small error in orientation 
can result in a big change to the Lorentz correction and thus to the corrected 
intensity. However, the default maximum reflection width can be changed 
(Experiment settings, Advanced Integration) and sometimes this is necessary to 
avoid excluding too many reflections in cases where the mosaic spread is very 
high (> 1° say) or the mosaic block size is small.

I think this feature is common to all integration programs, although the 
default settings may well be different.

Best wishes,

Andrew
On 14 Dec 2016, at 01:40, Hank  wrote:

> Dear CCP4BB users,
> 
> I have a question about Mosflm. The manual says green predictions have
> "reflection width greater than 5 degrees" and will not be integrated. I always
> assumed it should have something to do with Lorentz factor but not quite sure.
> Why is it so? I'm not aware of such geometrical restriction in HKL2000.
> Thank you!
> 
> Walt

Re: [ccp4bb] Why aren't green reflections on Mosflm integrated?

[Harry Powell]

Hi

Looking at this in a slightly different way:

The Lorentz factor is inversely related to the speed at which the reciprocal 
lattice points traverse the Ewald sphere; those reflections close to the 
rotation axis have a speed through the Ewald sphere that is tending towards 
zero (because they are moving more parallel to the surface of the Ewald 
sphere), so the Lorentz factor tends to infinity. Not only does the Lorentz 
factor get huge, but there comes the point computationally when the errors in 
calculating it get too big to get a meaningful value.

(There are also reflections that appear on the diffraction image even closer to 
the rotation axis that are due to reciprocal lattice points that are predicted 
to never completely cross the Ewald sphere, and these are not even marked by a 
green prediction.)

I imagine this sometimes as a meteoroid skimming across a planet's atmosphere 
(carrying straight on rather than bouncing off, perhaps passing through some of 
the atmosphere) but never reaching the surface (the thickness of the atmosphere 
would correspond to the thickness of the Ewald sphere). A meteoroid (moving at 
the same speed) encountering the atmosphere at an angle closer to 90º would 
pass through the atmosphere more quickly. This may or may not help...

On 14 Dec 2016, at 08:33, Tim Gruene wrote:

> Dear Walt,
> 
> reflections close to the rotation axis stay in reflecting condition for a 
> long 
> time, where time is sensibly measured in degrees. Their intensities cannot be 
> determined reliably, and I would think that most integrating programs, 
> including HKL2000, reject such reflections.
> 
> Best regards,
> Tim
> 
> 
> On Wednesday, December 14, 2016 10:40:31 AM Hank wrote:
>> Dear CCP4BB users,
>> 
>> I have a question about Mosflm. The manual says green predictions have
>> "reflection width greater than 5 degrees" and will not be integrated. I
>> always
>> assumed it should have something to do with Lorentz factor but not quite
>> sure.
>> Why is it so? I'm not aware of such geometrical restriction in HKL2000.
>> Thank you!
>> 
>> Walt
> -- 

Harry
--
Dr Harry Powell
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

Re: [ccp4bb] Why aren't green reflections on Mosflm integrated?

[Tim Gruene]

Dear Walt,

reflections close to the rotation axis stay in reflecting condition for a long 
time, where time is sensibly measured in degrees. Their intensities cannot be 
determined reliably, and I would think that most integrating programs, 
including HKL2000, reject such reflections.

Best regards,
Tim


On Wednesday, December 14, 2016 10:40:31 AM Hank wrote:
> Dear CCP4BB users,
> 
> I have a question about Mosflm. The manual says green predictions have
> "reflection width greater than 5 degrees" and will not be integrated. I
> always
> assumed it should have something to do with Lorentz factor but not quite
> sure.
> Why is it so? I'm not aware of such geometrical restriction in HKL2000.
> Thank you!
> 
> Walt
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/102
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

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[ccp4bb] 10 fully-funded 4 year PhD studentship in Non-Equilibrium Systems (CANES CDT)

[Lorenz, Chris]

Applications are now open for the CANES Programme
(September 2017 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 20 February 2017 for September 2017 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 £16,000 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