[ccp4bb] Refmac automatically handles twinning?

[Nicholas Keep]

Just double checking that Refmac automatically handles twinning without 
the need for a keyword or a box click in i2.  I have a crystal in P32 21 
that gives poor Rfactors and maps (Rfree mid 40s) from what should be an 
excellent model. I have reprocessed in P32, P1 and C2 but all give 
similar results so it appears not to be hidden twinning.  There is no 
need to click a box or enter a keyword for this to be a check for twinning ?


There is severe anisotropy and a few other problems flagged up in iSPYB 
so there may be more complex problems than twinning with these crystals


Best wishes

Nick

--
Prof Nicholas H. Keep
Emeritus Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

Dept email n.k...@bbk.ac.uk
Telephone 020-3926-3475  (Will contact me at home if working as well as my 
office)



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[ccp4bb] Online EM Course

[Nicholas Keep]

Please pass on to students/colleagues who may be interested.

The Department of Biological Sciences at Birkbeck, University of London 
is offering an on line, postgraduate course module on Macromolecular and 
Cellular Electron Microscopy, in the spring term January-March 2022. It 
will cover the basic principles of cryo-EM and image processing for both 
single particle and tomography approaches. It can be taken as a stand 
alone module or as part of the MSc in Structural Biology. The course is 
taught by cryo-EM experts and runs in six 2 week sessions, each with 
quizzes, marked coursework and a live tutorial, and students are 
assessed by a final exam in additional to their coursework.
The course is suitable for those wanting to understand or use structural 
biology research using cryo-EM, in academia or industry.


More information and registration:
https://www.bbk.ac.uk/study/2021/short-courses/modules/scbs/SCBS061S7

--
NOTE NEW PHONE NUMBER JULY 2020

I do not work Mondays.  For urgent business on a Monday contact Clare Woodward 
(Director of Operations) or Gillian Forrester (Deputy Dean)

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

Office G54a

Dean Email;scid...@bbk.ac.uk
Dept emailn.k...@mail.cryst.bbk.ac.uk
Telephone 020-3926-3475  (Will contact me at home if working as well as my 
office)

If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door



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Re: [ccp4bb] A "funny" thing related to AlphaFold2 ....

[Nicholas Keep]

Has anyone made use of an Alpha Fold PDB as opposed to CIF.  On the half 
dozen or so I have tried to read into CCP4mg or coot the PDB has always 
failed but the CIF is fine.  I can then write out a PDB if I want.


I could add to the conspiracy theories that this is EBI trying to 
normalise use of CIF format, but I suspect it is something much more 
mundane, that should be addressed.


Best wishes

Nick

--
NOTE NEW PHONE NUMBER JULY 2020

I do not work Mondays.  For urgent business on a Monday contact Clare Woodward 
(Director of Operations) or Gillian Forrester (Deputy Dean)

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

Office G54a

Dean Email;scid...@bbk.ac.uk
Dept email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-3926-3475  (Will contact me at home if working as well as my 
office)

If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door



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[ccp4bb] Distance Learning Structural Biology Modules

[Nicholas Keep]

The taught modules of the Birkbeck, University of London MSc in 
Structural Molecular Biology are now available as single modules for 
Continuous Professional Development (CPD).


The modules are in

Protein Crystallography 



Macromolecular and Cellular Electron Microscopy 



Protein Structure Determination 



Protein Expression, Purification and Biophysical Characterisation 



Principles of Protein Structure 



Protein Bioinformatics 



More details can be found clicking the links above or searching at 
https://www.bbk.ac.uk/ if the links do not come through on email.


Birkbeck has a long tradition in Structural Biology and former staff 
include JD Bernal, Rosalind Franklin, Aaron Klug and Tom Blundell.  We 
have been teaching Structural Biology via the World Wide Web since 1996 
and have recently moved to a new Virtual Learning Environment.  There 
are live online tutorials with our expert staff as well as online course 
material, course work and a final exam


Do contact me for further details

Nick

--
NOTE NEW PHONE NUMBER JULY 2020

I do not work Mondays.  For urgent business on a Monday contact Clare Woodward 
(Director of Operations) or Gillian Forrester (Deputy Dean)

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

Office G54a

Dean Email;scid...@bbk.ac.uk
Dept email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-3926-3475  (Will contact me at home if working as well as my 
office)

If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door




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[ccp4bb] Question about P3, H3 and R3 space groups

[Nicholas Keep]

I have an answer from Jeremy Cockcroft the author of the 'Birkbeck' 
Tables. Actually Jeremy has been at UCL for a decade or so and they are 
hosted from their


Nick

In answer to the question regarding the use of R and H for trigonal 
space groups, the letters refer to two distinct types of lattice 
centring symmetry operation, namely +(⅓,⅔,⅔), +(⅔,⅓,⅓) and +(⅓,⅔,0), 
+(⅔,⅓,0), respectively. For the subset of rhombohedral space groups, the 
symbol R should always be used.When the alternative unit cell with a=b=c 
and α=β=γ is chosen, this cell corresponds to a primitive Bravais 
lattice, but the label P is not used as this would result in confusion 
with non-rhombohedral space groups. (The choice of symmetry operators 
for rhombohedral space groups is wholly dependent of the choice of unit 
cell, i.e. hexagonal versus rhombohedral, so there is no ambiguity if 
the unit cell is specified.)


For the non-rhombohedral space groups, it may occasionally be convenient 
to choose a larger H-centred unit cell that is not the usual primitive P 
one.(The use of larger unit cells is quite common for systems that 
undergo phase transformations as it may enable the crystallographer to 
keep the contents of the unit cell the same in both phases.)Note that 
the use of an H-centred lattice switches the order of the symmetry 
elements in these space group symbols, e.g. P312 becomes H321.


I am not aware of any changes to this convention, which I believe has a 
long history. However, it is possible that the letter H has been used 
unwittingly for other purposes.


Jeremy Karl Cockcroft


--

NOTE NEW PHONE NUMBER JULY 2020

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

Office G54a

Dean Email; scid...@bbk.ac.uk
Dept email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-3926-3475  (Will contact me at home if working as well as my 
office)

If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door




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[ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

[Nicholas Keep]

We are going to be doing a data collection for an MRes student at 
Diamond in the next couple of weeks.  These are his first crystals.  It 
would be good if he could be involved in watching it.


I was wondering if anyone had tried sharing screen and voice via moodle 
collaborate or Microsoft Teams while doing a data collection?  Zoom is 
deprecated by our institution but if anyone had succeeded on zoom that 
would also be interesting.


I am on Virgin media 100 MB broadband which is pretty much achieving 
that (upload is only around 9 MB though).


Alternatively we can try and set him up to connect via nx and watch, but 
that would lose the sound connection unless I have a phone tucked under 
my chin.


We could just record my screen and sound and he could watch later.

Any tips?

Best wishes

Nick



--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

Dean Email; scid...@bbk.ac.uk
Dept email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door



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[ccp4bb] Average B factors with TLS

[Nicholas Keep]

I am at the point of depositing a low resolution (3.15 A) structure 
refined with REFMAC.  The average B factors were 31 before I added the 
TLS contribution as required for deposition which raised them to 157- 
this is flagged as a problem with the deposition, although this did not 
stop submssion.  The estimated Wilson B factor is 80.5 (although that 
will be quite uncertain) so somewhere between these two extremes.


Is it only the relative B factors of the chains that is at all 
informative?  Should I report the rather low values without TLS 
contribution or the rather high ones in any "Table 1"?  Comments 
appreciated.


Thanks

Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

Dean Email; scid...@bbk.ac.uk
Dept email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door



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[ccp4bb] CCP4i2 London Road Show

[Nicholas Keep]

Reminder CCP4i2 London Road show  TOMORROW.  Places still available.

*CCP4 i2 Road Show, London*

There will be a CCP4 Road Show for use of the i2 interface on Tuesday 
12th November, at Birkbeck College.
*Time:* 14:00 - 16:00 for the main workshop with about an hour 
afterwards for those with additional questions.

*Place:* Room 416 in the main Birkbeck Malet St Building.
There will be 2-3 CCP4 tutors presenting the Road Show.
While it is primarily intended for the extensive number of 
crystallographers in London, all are welcome.
There will be places for 40 participants. Desktops will be used, but you 
are also welcome to use your laptops (but if doing so please ensure 
you install the software in advance - see CCP4 webpages for guidance on 
how to do this).


To book a place on a first come first served basis please register at 
http://www.bbk.ac.uk/booking/event/8829


Event page is http://www.bbk.ac.uk/events/remote_event_view?id=8829

Best wishes

Nick Keep and Keith Wilson

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

emailn.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door




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[ccp4bb] Fwd: CCP4i2 London Road Show

[Nicholas Keep]

Reminder One week to London CCP4i2 Road show.  Places still available.

*CCP4 i2 Road Show, London*

There will be a CCP4 Road Show for use of the i2 interface on Tuesday 
12th November, at Birkbeck College.
*Time:* 14:00 - 16:00 for the main workshop with about an hour 
afterwards for those with additional questions.

*Place:* Room 416 in the main Birkbeck Malet St Building.
There will be 2-3 CCP4 tutors presenting the Road Show.
While it is primarily intended for the extensive number of 
crystallographers in London, all are welcome.
There will be places for 40 participants. Desktops will be used, but you 
are also welcome to use your laptops (but if doing so please ensure 
you install the software in advance - see CCP4 webpages for guidance on 
how to do this).


To book a place on a first come first served basis please register at 
http://www.bbk.ac.uk/booking/event/8829


Event page is http://www.bbk.ac.uk/events/remote_event_view?id=8829

Best wishes

Nick Keep and Keith Wilson

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

emailn.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door




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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Fwd: [Labmanagers] CCP4i2 London Road Show

[Nicholas Keep]

Reminder Two weeks to London CCP4i2 Road show.  Places still available.

*CCP4 i2 Road Show, London*

There will be a CCP4 Road Show for use of the i2 interface on Tuesday 
12th November, at Birkbeck College.
*Time:* 14:00 - 16:00 for the main workshop with about an hour 
afterwards for those with additional questions.

*Place:* Room 416 in the main Birkbeck Malet St Building.
There will be 2-3 CCP4 tutors presenting the Road Show.
While it is primarily intended for the extensive number of 
crystallographers in London, all are welcome.
There will be places for 40 participants. Desktops will be used, but you 
are also welcome to use your laptops (but if doing so please ensure 
you install the software in advance - see CCP4 webpages for guidance on 
how to do this).


To book a place on a first come first served basis please register at 
http://www.bbk.ac.uk/booking/event/8829


Event page is http://www.bbk.ac.uk/events/remote_event_view?id=8829

Best wishes

Nick Keep and Keith Wilson

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

emailn.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] CCP4i2 London Road Show

[Nicholas Keep]

*CCP4 i2 Road Show, London*

There will be a CCP4 Road Show for use of the i2 interface on Tuesday 
12th November, at Birkbeck College.
*Time:* 14:00 - 16:00 for the main workshop with about an hour 
afterwards for those with additional questions.

*Place:* Room 416 in the main Birkbeck Malet St Building.
There will be 2-3 CCP4 tutors presenting the Road Show.
While it is primarily intended for the extensive number of 
crystallographers in London, all are welcome.
There will be places for 40 participants. Desktops will be used, but you 
are also welcome to use your laptops (but if doing so please ensure 
you install the software in advance - see CCP4 webpages for guidance on 
how to do this).


To book a place on a first come first served basis please register at 
http://www.bbk.ac.uk/booking/event/8829


Event page is http://www.bbk.ac.uk/events/remote_event_view?id=8829

Best wishes

Nick Keep and Keith Wilson

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door




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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Cif deposition from CCP4i2

[Nicholas Keep]

I am not quite sure if this is a bug report, or advice for other people 
or what.


Essentially I wanted an mmCIF of a refmac refined structure for 
deposition.  The CCp4i2 "prepare files for deposition" gives an mmcif 
with a Rfree several % higher than my best refinement. Essentially this 
appears to be the result of a zero cycles run of refmac.   Giving the 
output TLS file (from runs that produce output with or without added 
contribution to B factors) does not solve this problem


However the latest upgrade of ccp4 does give an MMCIF from the Refmac 
job that can be exported with the desired Rfactors.


Presumably this is the route to deposit.  What is the purpose then of 
the "Prepare files for deposition job" in terms of cordinates.  The 
reflections cif file is useful.


Best wishes

Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door



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Re: [ccp4bb] Unknown density

[Nicholas Keep]

There is no blue (2fo-fc) density at least at the current contour level 
in your difference density.  That probably indicates what you are seeing 
is noise rather than a real feature.


I am also seeing more intense (above 7 sigma in some cases) positive 
difference density without actual density in my current refmac refined 
structure than I am used to.


I ascribed this to being in P1 with significant anisotropy leading to 
ripples???, but if this is widespread then there may have been tweaks to 
the software.  Anyone else want to comment on this


Best wishes

Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door



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[ccp4bb] Molprobity "Feature" in ccp4i2 refmac

[Nicholas Keep]

I have found a 'feature' in molprobity.  if there are two atoms on top 
of each other (not hard to do by mistake when adding waters in coot), 
then molprobity does not work or at least does not give the outputs 
required to then give the coot molprobity checklist file our of the 
ccp4i2 refmac interface.  A check at some point for this mistake would 
be good to throw out a clear error message.


Best wishes

Nick


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door



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[ccp4bb] Java based structural database websites

[Nicholas Keep]

This is slightly off topic but I suspect people from PDBe etc read this 
bulletin board.


Quite a number of very useful structural biology web sites (Olderado, 
Vivaldi, EMDB to name but a few) require java based viewers and hence no 
longer have full (or in the case of vivaldi any) functionality on up to 
date browsers.


On a new computer it may prove hard or even impossible to find a browser 
that will work


Are there plans to update these websites and is there any suggeted time 
scale?


Any work rounds?

Best wishes

Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Director of Institute for Structural and Molecular Biology at UCL/Birkbeck

[Nicholas Keep]

We are looking to recruit a world leading scientist to succeed Prof 
Gabriel Waksman FRS FMedSci as Director of the Institute of Structural 
and Molecular Biology at UCL and Birkbeck, University of London.


The Institute of Structural and Molecular Biology (ISMB) is a 
world-leading interdisciplinary institute in the field of structural, 
molecular and mechanistic biology, and an important strategic 
collaboration between UCL and Birkbeck, University of London. Research 
interests cover a broad range of key research questions in fundamental 
biology, with a particular focus on the mechanisms of molecular 
machines. Our approaches are at the cutting edge of interdisciplinary 
biomolecular science. World-class research facilities are accessible to 
all ISMB members, including laboratories for cryo-electron microscopy, 
X-ray crystallography, NMR spectroscopy, biophysical methods, mass 
spectrometry, computational biology, cell biology, optical microscopy 
and microbiology. ISMB seminars, symposia and retreats facilitate 
collaborative research activities, while our PhD programmes, including 
an ISMB Wellcome Trust funded programme, support recruitment of 
high-calibre students committed to interdisciplinary research.  The 
successful candidate will have a world-class record of research in a 
complementary area, a shared commitment to multidisciplinary and 
multiscalar approaches to mechanistic biology, and a vision to lead the 
ISMB to the next stage of its development.


Details and the application form can be found at
https://atsv7.wcn.co.uk/search_engine/jobs.cgi?SID=amNvZGU9MTczNDQwNCZ2dF90ZW1wbGF0ZT05NjUmb3duZXI9NTA0MTE3OCZvd25lcnR5cGU9ZmFpciZicmFuZF9pZD0wJnBvc3RpbmdfY29kZT0yMjQ=

For informal enquiries, please contact Professor Frances Brodsky 
(Director, UCL Biosciences and Chair of the Search Committee 
(f.brod...@ucl.ac.uk <mailto:f.brod...@ucl.ac.uk>) or, for enquiries 
about Birkbeck, Professor Nicholas Keep (n.k...@bbk.ac.uk 
<mailto:n.k...@bbk.ac.uk>).


Closing Date 31st July 2018



--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

emailn.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Support for Mosquito Robots

[Nicholas Keep]

Does anyone (particularly in the UK) have their Mosquito robot 
maintained by anyone other than TTP labtech the manufacturers?


Our procurement people want to see if there are any other providers.

Thanks

Nick


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Fwd: X-ray Lab Manger Birbeck University of London- Permanent Post

[Nicholas Keep]

A reminder this vacancy closes on Sunday.

There is a vacancy for an X-Ray Laboratory Manager at the Institute for 
Structural and Molecular Biology at Birkbeck/UCL based at Birkbeck, 
University of London.


see https://tinyurl.com/y7jgfmr5

This is a permanent University Funded post.  A brief description of the 
role is below and informal enquiries can be made to me 
(n.k...@mail.cryst.bbk.ac.uk). Closing date is the end of the 10th 
December 2017.


Best wishes

Nick


The Laboratory Manager role will ensure efficient day-to-day running of 
the X-ray Laboratory (including X-ray generators, detectors and 
crystallisation robots) for research staff and students in Biological 
Sciences, the ISMB and for external collaborators and hirers of the 
equipment; ensure that all safety procedures in the laboratory are 
implemented; provide training in use of equipment and to give general 
assistance in crystallography to students and research staff; keep 
abreast of new technologies and methodologies and assess and advise on 
the purchase of new equipment, software, and reagents.
The role holder will coordinate trips to synchrotrons and organise 
Beamline applications. The role holder will also contribute to teaching 
in the department through design, deliver and supervision of practicals, 
tutorials and projects in the general area of molecular biology and 
crystallography


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

emailn.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] X-ray Lab Manger Birbeck University of London- Permanent Post

[Nicholas Keep]

There is a vacancy for an X-Ray Laboratory Manager at the Institute for 
Structural and Molecular Biology at Birkbeck/UCL based at Birkbeck, 
University of London.


see https://tinyurl.com/y7jgfmr5

This is a permanent University Funded post.  A brief description of the 
role is below and informal enquiries can be made to me 
(n.k...@mail.cryst.bbk.ac.uk).  Closing date is the end of the 10th 
December 2017.


Best wishes

Nick


The Laboratory Manager role will ensure efficient day-to-day running of 
the X-ray Laboratory (including X-ray generators, detectors and 
crystallisation robots) for research staff and students in Biological 
Sciences, the ISMB and for external collaborators and hirers of the 
equipment; ensure that all safety procedures in the laboratory are 
implemented; provide training in use of equipment and to give general 
assistance in crystallography to students and research staff; keep 
abreast of new technologies and methodologies and assess and advise on 
the purchase of new equipment, software, and reagents.
The role holder will coordinate trips to synchrotrons and organise 
Beamline applications. The role holder will also contribute to teaching 
in the department through design, deliver and supervision of practicals, 
tutorials and projects in the general area of molecular biology and 
crystallography


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

emailn.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

[Nicholas Keep]

I must also credit Robbie with the easiest (most elegant?) solution to 
my question.


You run 0 cycles of refmac with the mixed B factor model.

Thanks all for your inputs.

Best wishes

Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

[Nicholas Keep]

It would be nice to be able to run zero cycles of refmac to get a map 
etc direct from a PDB file.


However due the PDB requiring the TLS component of B factor to be 
included this does not work.


Is there software to remove the TLS component so a zero cycle of refmac 
can be run.


Best wishes

NIck


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Career Development Fellows in the ISMB, Birkbeck University of London

[Nicholas Keep]

   Birkbeck, University of London has three vacancies for Career
   Development Fellows for up to three years funded by Wellcome ISSF
   funding. These posts may be held part-time or full-time.

   
http://jobs.bbk.ac.uk/fe/tpl_birkbeckcollege01.asp?s=4A515F4E5A565B1A=62982,3483792359=109179339=98996182342315=secehisboccgnqexww


   Deadline March 19th 2017

   This is an opportunity for talented researchers to develop their own
   research program and apply for long term fellowships. Structural
   Biology is a particular strength at Birkbeck through the Institute
   for Structural and Molecular Biology www.ismb.lon.ac.uk/.
   Applications are sought from candidates with an exciting project and
   a strong publication record.  For informal inquiries please contact
   Prof Gabriel Waksman, the Director of the ISMB
   (g.waks...@mail.cryst.bbk.ac.uk)


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

Re: [ccp4bb] How many is too many free reflections?

[Nicholas Keep]

I agree with Gerard.  It would be much better in many ways to generate a 
separate file of Free R flags for each crystal form of a project to some 
high resolution that is unlikely to ever be exceeded eg 0.4 A that is a 
separate input file to refinement rather than in the mtz.



The generation of this free set could ask some questions like is the 
data twinned, do you want to extend the free set from a higher symmetry 
free set.  eg C2 rather than C2221 (symmetry is close to the higher 
symmetry but not perfect- seems to happen not infrequently).


Could some judicious selection of sets of related potentially related 
hkls work as a universal free set? (Not thought this through fully)


This would get around practical issues like I had yestserday in refining 
in another well known package where coot drew the map as if it was 0.5 
A data even though there were only observed data to 2.1 the rest just 
being a hopelessly overoptimistic guess of the best ever dataset we 
might collect.


I agree you CAN do this with current software- it is just not the path 
of least resistance, so you have to double check your group are doing this.


Best wishes
Nick





--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Graphic for rotation about axis

[Nicholas Keep]

Where can you get hold of a graphic that indicates a rotation around the 
horizontal or vertical axis
These occur in a lot of papers to indicate the relation between two 
views but I don't seem to easily be able to google how to get hold of them

best wishes
Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Career Development Fellow Birkbeck University of London

[Nicholas Keep]

Birkbeck, University of London has a long tradition in structural 
biology going back to JD Bernal.  As part of the institute for 
Structural Molecular Biology http://www.ismb.lon.ac.uk/ under Prof 
Gabriel Waksman FRS, it remains a leading centre in the UK for 
structural biology.


 The college is using part of its Wellcome Institutional Strategic 
Support Fund to hire up to 3 two year career development fellows. This 
is to allow an early career researcher to develop an idea, including 
collecting preliminary data, to the stage where they would be 
competitive for a Wellcome or other funding body early career 
researchers.  The application should include an outline of the research 
plans as well as a description of previous experience.


The advert can be found at
http://jobs.bbk.ac.uk/fe/tpl_birkbeckcollege01.asp?s=4A515F4E5A565B1Ajobid=55528,9858157887key=85249108c=525423345221pagestamp=sexomqdrzqtzrakcse
The deadline is 10th December 2014.

Informal enquires can be made to Prof Waksman 
g.waks...@mail.cryst.bbk.ac.uk


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Two Molecular Biology Lab Manager Positions

[Nicholas Keep]

Birkbeck, University of London has two vacancies to mange our Molecular 
Biology research laboratories.  The post holders are responsible for 
ordering, equipment maintenance and health and safety.  They will also 
be involved in development of teaching laboratory practicals and 
assisting in research and supervision of Phd and undergraduate and 
masters projects as their other duties allow.
More details and applications can be found at 
http://www.jobs.ac.uk/job/AJA852/research-laboratory-manager-two-posts/ 
with a closing date of the 28th July.


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Loop clashing on symmetry axis

[Nicholas Keep]

Am refining a structure in P3(1)21 with three copies in the ASU. It is 
pretty close to completion R/Rfree 18/21 with 2A data.
However in one copy a section that is clear in the other two is poor as 
it meets itself on a two fold.


My interpretation is that one copy of the loop is in a visible 
conformation that is on the two fold axis and the symmetry related copy 
is disordered so it does not clash. Presumably close to half the time 
the ordered copy is from one side and the rest from the other to give 
the symmetric density.



If you push the structure into the density then the symmetry related 
copy clashes.


Is this conformation refineable in refmac5 or phenix if the occupancy is 
set to zero?


Should I allow clashes to push both copies either side of the density as 
is currently happening?


Any tips on dealing with this?

Best wishes
Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

Re: [ccp4bb] Loop clashing on symmetry axis

[Nicholas Keep]

On 10/06/2014 18:48, Nicholas Keep wrote:

is set to zero

Sorry in my last email this should read  is set to a fraction eg 0.5

Nick
Am refining a structure in P3(1)21 with three copies in the ASU. It is 
pretty close to completion R/Rfree 18/21 with 2A data.
However in one copy a section that is clear in the other two is poor 
as it meets itself on a two fold.


My interpretation is that one copy of the loop is in a visible 
conformation that is on the two fold axis and the symmetry related 
copy is disordered so it does not clash. Presumably close to half the 
time the ordered copy is from one side and the rest from the other to 
give the symmetric density.



If you push the structure into the density then the symmetry related 
copy clashes.


Is this conformation refineable in refmac5 or phenix if the occupancy 
is set to zero?


Should I allow clashes to push both copies either side of the density 
as is currently happening?


Any tips on dealing with this?

Best wishes
Nick


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

Re: [ccp4bb] Bfactors too high after TLS refinement

[Nicholas Keep]

TLS in phenix does seem to lead to high B factors in some of our cases. 
To check whether it was particular to our datasets , we rerefined some 
similar structures to ours  from the PDB and found that their B factors 
increased to high values similar to our structure when run through the 
same phenix.refine protocol.


Structure 1 Chain A original Average B 40.85 After Phenix with TLS 
113.33 Chain B Original 50.1 After phenix TLS 121.11
Structure 2 Chain A original Average B 64.46  After Phenix with TLS 
100.63 Chain B original 64.99 After Phenix TLS 103.5
Structure 3 Chain A original 46.44 After TLS 52.63 - so it does not 
always happen


This of course only proved that our data was probably not exceptional it 
was the protocol.   It does not explain what is going on.


http://www.phenix-online.org/pipermail/phenixbb/2010-January/014374.html
seems to offer some explanation of the TLS scaling in phenix.

It may be the anisotropic component reduces the size of the actual B 
factor back to closer to the values before TLS?


Best wishes
Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Britton/Murray Rust plot

[Nicholas Keep]

I am confused by the Britton/Murray-Rust plots in ctruncate.
My reading this morning has indicated that the Britton plot was 
actually proposed by Fisher and Sweet 1980. Treatment of diffraction 
data from crystals twinned by merohedry. Acta Crystallogr.A36:755--760 
and plots the fraction of negative intensities after detwinning which 
increases rapidly above the twin fraction.


The more often quoted Britton (1972) Acta A28 296-297 actually plot 
I(2)/(I(1)+(I2)  where I(1) and I(2) are twin related intensities and 
the lowest value is the twin fraction


and Murray-Rust, P. (1973) Acta Cryst B29, 2559-2566  plot(F(1) against F(2) 
which is bounded by lines of slope sqrrt[(1-twin)/(twin)] and 
sqrrt[twin/(1-twin)]

Is then the ctruncate Murray-Rust Britton plot a detwin of F rather than I or 
something else not documented (as far as I can find).

The documentation of the software does not seem to explain nor credit Fisher 
and Sweet

Can anyone enlighten me as to the differences in the Britton plots in ctruncate.
Thanks
Nick


---
Prof Nicholas H. Keep Executive Dean of School of Science Professor of 
Biomolecular Science Crystallography, Institute for Structural and 
Molecular Biology, Department of Biological Sciences Birkbeck, 
University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email 
n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 
020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to 
access me in person you have to come to the crystallography entrance and 
ring me or the department office from the internal phone by the door

Re: [ccp4bb] Table in NSMB

[Nicholas Keep]

I would have thought that ligands are ligand/ion?.  What I have just 
done with a recent structure and I await the reviewers noticing or not 
is include the ethylene glycol from the cryo that I can (probably) see 
in a solvent (rather than water) atom number and bfactor line along with 
water (which probably includes sodium/chloride ions etc misassigned as 
water) rather than as ligand.
I would suggest that  Protein, Ligand, Solvent/Ion is probably a better 
break down than Protein, Ligand/Ion and Water alhtough if I had an ion 
associated with a ligand  Mg on my ATP I would have that in ligand 
rather than ion.  What then should you do if there are waters then 
visible on the ion???
I guess the question that this is really asking is whether the Bfactor 
of what you are describing as a significant ligand in your discussion is 
well ordered compared to the surrounding protein.
Gubbins filling out density peaks in the solvent area probably should 
not be included in that line.

Best wishes
Nick

--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

Re: [ccp4bb] Table in NSMB

[Nicholas Keep]

Sorry misread the initial post.  Yes a protein ligand should be in the 
protein but you could give B factor number for each chain- my comments 
about what goes in ligand and what in solvent may be of general 
interest/comment

Nick

--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

Re: [ccp4bb] Unidentified blobs

[Nicholas Keep]

It is most likely to be something in your crystallisation condition, 
your cryoprotectant, or the buffer you stored your protein in.

Could be a detergent carried through several steps of purification
Could for example be some part of a PEG molecule that gets ordered round 
a more hydrophobic bit of your protein surface.
You need to think about everything your protein has come into contact 
with, possibly even inside the cell.  It is not uncommon to carry 
cofactors right through a purification, less likely in something more 
surface bound like this.

Best wishes
Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the 
crystallography entrance

and ring me or the department office from the internal phone by the door

[ccp4bb] Fwd: [ccp4bb] Structural Biologist Central London_ DEADLINE VERY SOON

[Nicholas Keep]

*Structural Biologist *

*Location: Central London, UK*

*12 month fixed-term contract*

*Salary dependent on experience*

**

Cancer Research Technology (CRT) is a specialist drug discovery,
technology transfer and commercialisation company which aims to advance
new discoveries to beat cancer. At the present time CRT employs some 140
people, including a large complement of scientists and business
development specialists across multiple sites in the UK, with close
partnerships working with associated operations in the USA. As a wholly
owned subsidiary of Cancer Research UK, we have extensive experience in
developing and licensing oncology related opportunities with world-class
pharmaceutical and biotechnology companies.

To help achieve this goal, the CRT Discovery Laboratories based in
Central London and Cambridge aim, through multidisciplinary teams of
scientists, to undertake drug discovery programmes on exciting novel
cancer targets to develop small moleculetherapies.

We are seeking to recruit a highly motivated protein scientist /
structural biologist to join our X-ray structure determination team.The
team has access to state-of-the-art data collection and crystallization
facilitieswithinthe School of Crystallography, Birkbeck College, London
and is adjacent to CRT’s Discovery Laboratories within the Wolfson
Institute of Biomedical Research, University College London.

The successful candidate should have experience in one or more of the
following areas:

  * Production and characterization of crystallization-grade protein for
structural analysis
  * Crystallization screening and optimization of protein-ligand complexes
  * X-ray data collection and structure determination

You should ideally be qualified to PhD level or equivalent. In addition,
you will possess excellent communication and organisation skills, and
will be able to contribute positively to interactive collaborations
within CRT, Cancer Research UK laboratories and other external
organisations.Previousexperience within a pharmaceutical environment
would be desirable.

Please note that applications will only be accepted from candidates who
have proof of their right to work in the U.K.

To apply, please send a copy of your CV and a covering letter, *quoting
the reference number XR1304*, to the Head of Medicinal Chemistry by
email to crtrecruitm...@cancertechnology.com
mailto:crtrecruitm...@cancertechnology.com

*Closing Date: 6^th May 2013*//

/No Agencies/**

/CRT is an equal opportunities employer/



--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the 
crystallography entrance

and ring me or the department office from the internal phone by the door

[ccp4bb] Structural Biologist Central London

[Nicholas keep]

*Structural Biologist *

*Location: Central London, UK*

*12 month fixed-term contract*

*Salary dependent on experience*

**

Cancer Research Technology (CRT) is a specialist drug discovery, 
technology transfer and commercialisation company which aims to advance 
new discoveries to beat cancer. At the present time CRT employs some 140 
people, including a large complement of scientists and business 
development specialists across multiple sites in the UK, with close 
partnerships working with associated operations in the USA. As a wholly 
owned subsidiary of Cancer Research UK, we have extensive experience in 
developing and licensing oncology related opportunities with world-class 
pharmaceutical and biotechnology companies.


To help achieve this goal, the CRT Discovery Laboratories based in 
Central London and Cambridge aim, through multidisciplinary teams of 
scientists, to undertake drug discovery programmes on exciting novel 
cancer targets to develop small moleculetherapies.


We are seeking to recruit a highly motivated protein scientist / 
structural biologist to join our X-ray structure determination team.The 
team has access to state-of-the-art data collection and crystallization 
facilitieswithinthe School of Crystallography, Birkbeck College, London 
and is adjacent to CRT's Discovery Laboratories within the Wolfson 
Institute of Biomedical Research, University College London.


The successful candidate should have experience in one or more of the 
following areas:


 * Production and characterization of crystallization-grade protein for
   structural analysis
 * Crystallization screening and optimization of protein-ligand complexes
 * X-ray data collection and structure determination

You should ideally be qualified to PhD level or equivalent. In addition, 
you will possess excellent communication and organisation skills, and 
will be able to contribute positively to interactive collaborations 
within CRT, Cancer Research UK laboratories and other external 
organisations.Previousexperience within a pharmaceutical environment 
would be desirable.


Please note that applications will only be accepted from candidates who 
have proof of their right to work in the U.K.


To apply, please send a copy of your CV and a covering letter, *quoting 
the reference number XR1304*, to the Head of Medicinal Chemistry by 
email to crtrecruitm...@cancertechnology.com 
mailto:crtrecruitm...@cancertechnology.com


*Closing Date: 6^th May 2013*//

/No Agencies/**

/CRT is an equal opportunities employer/

[ccp4bb] P212121 and P213

[Nicholas Keep]

I have a structure which normally crystallises in P213 but one data set
the edges became slightly non-equivalent in length by a couple of
angstroms and the data process in P212121

P212121 symmetry operators appears to be a subset of P213

http://img.chem.ucl.ac.uk/sgp/large/019az1.htm
http://img.chem.ucl.ac.uk/sgp/large/198az1.htm

(Not absolutely sure the above are world viewable)

Naively I expected the two structures to roughly align.  However they
don't there appears to be some change of axes between them.
The transform of the P213 onto the P212121 structure is
0.03345 -0.9977 -0.0598
-0.9994 0.03402 -0.08653
0.01066 0.05929  -0.9982
-18.16 -57.18 21.39

This is clearly close to

0 -1 0
-1 0 0
0 0 -1
-0.25 -.75 0.25 in fractionals.

Applying either the exact transformation or the regularised one
with ether indexing of  p213 ie original and k h -l
http://www.ccp4.ac.uk/html/reindexing.html
the rfactors are well above 50% and don't drop.

Any suggestions of what I am doing wrong or is this not going to work
(tried MR into the reindexed data and that does not align either- in 
fact I have tried quite a lot things)


The reason for trying to get the two structures on the same axes is to
compare the electron densities.  The P212121 seems to have some of the
disorder loops better defined.

Using the Coot transform map by LSQ superpose is quite good BUT it would
be better if it were another map other than the refinement map that is
transformed as I then want to refine the unmoved structure into the
unmoved map guided by the moved map and that involved a lot of changes 
of map selection.


Thanks
nick



--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the
crystallography entrance
and ring me or the department office from the internal phone by the door


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the 
crystallography entrance

and ring me or the department office from the internal phone by the door

Re: [ccp4bb] P212121 and P213

[Nicholas Keep]

Thanks Eleanor, your tip has got me there. I was attempting the problem 
the wrong way round.


To get it to work

I had to reindex the P212121  h=-l k=k l=h
Then rigid body refinement of the P213 symmetry generated trimer dropped 
it to 40% and NCS refinement to around 25%


My reasoning for avoiding doing it this way round is that presumably if 
we deposit the P213 and the P212121 structures the wwPDB will reset to 
abc (I seem to remember)


A quick go at trying to reverse this has not worked.  Maybe the radius 
of convergence of a rigid body is lower in the higher symmetry space 
group??



For info
In P213  a=b=c 75.953
P212121 a=74.504 b=77.473 c=79.894


The SSM fit is 0.79 over virtually all Calphas for the symmetry 
generated trimer in P213 onto the P212121 structure



In response to Herman
The final P213 data set is actually higher resolution (we have collected 
several of these at a range of resolution as we improved cryo/crystal 
size/sampled more crystals/cooling pathways).  The P212121 was the 
highest at one point and has better density for some loops.


Many thanks to all who sent me hints

Nick





--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the 
crystallography entrance

and ring me or the department office from the internal phone by the door

Re: [ccp4bb] PEG refinement

[Nicholas Keep]

I doubt there is a consensus on this.  Your PEG solution is a mixture of 
lengths of polymer and normally you can only see a small fraction of the 
PEG molecule.  PEG400 will be between 8 and 10 ethylene glycols.  Bigger 
PEGS probably vary more.  My experience is that you can often only see 
density for 3-6 ethylene glycol units (and this is probably not related 
to whether the PEG is 400, 4K or 20K). You select the length of PEG that 
matches your density rather than being a function of what is in the 
crystallisation
 The argument would be I guess that a hydrophobic patch makes a section 
of the ethylene glycol ordered enough to be seen as density but the 
extensions occupy a sufficient range of conformations as to appear 
disordered.  I have put short stretches of PEG as it seems to be the 
best interpretation of difference density but I do always wonder if it 
is real or some kind of Fourier termination effect or partially ordered 
waters etc.  I would be cautious about basing too much biology on it.

Nick


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the 
crystallography entrance

and ring me or the department office from the internal phone by the door

Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore

[Nicholas keep]

I think Fred is overstating the problem of compulsory adverts. There are 
also cases where the expected pre-selected candidate does not get the 
job as a better candidate appears. There are also cases where there is 
eventually no job for anyone. Another outcome of an interview is you 
don't get the advertised post but are mentored through a fellowship 
application or similar to that institution. Like not stating an age 
range compulsory adverts are practices designed to reduce prejudice or 
nepotism, but do not eliminate it. They do not completely change the 
attitude of panel members, but most scientists do look at the data in 
front of them. The system also works both ways, you get good candidates 
coming for a job, who are only after an offer to improve their pay 
negotiations at their home institute. Nick



--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science Crystallography,
 Institute for Structural and Molecular Biology,
Department of Biological Sciences Birkbeck,
University of London,
Malet Street, Bloomsbury
LONDON WC1E 7HX

[ccp4bb] Merging hi and low res data

[Nicholas Keep]

We have a high and low res pass on a crystal that is going to around 1.2 A on 
the pilatus at Diamond.
We tried to scale them together using the xds CORRECT files from the xia2 -3dii runs (gives best results as far as we 
can see comparing xia2.html files)  through aimless via ccp4i interface.


The combined dataset looks worse (based on merging statistics at lower resolutions) than the individual particular at 
low res.(Compared to scala xia2 runs).

XDS does not record the pilatus as having overloads even on the high res pass 
using the correct detector parameters
http://xds.mpimf-heidelberg.mpg.de/html_doc/detectors.html

What I wanted to do was limit the resolution of the two runs ie to use low res between 100-2.5 beyond which completeness 
plummets and then the highres between 8 and 1.2.  Aimless does not seem to allow me to do that at least by the ccp4i 
interface- is this then bad practice?  I guess I could run a utility to remove the resolutions I don't want.


The one effect that makes me wonder if the lowres is better data, and worth combining, ie there is some overload in the 
high res, is that it goes from 30-8 mean I/SIGI whereas the high res has I/SIGI of 15 in most of the low res shells and 
then slowly falls off to 2.0 at 1.2 angstrom.


Am intending to carry on just using the hires pass.

Any comments?

I think Phil is in NZ and not looking at email hence putting this to the whole 
community
--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

Re: [ccp4bb] Creating CIF Files and Renaming Ligands

[Nicholas Keep]

Did you rename the ligand in the CIF file as well?  It would be nice if the Prodrg interface allowed you to type in the 
name of the ligand you want in the CIF and PDB file.  Hopefully a global replace in your favourite text editor of DRG 
with LIG or whatever you want to call your ligand would work.  You would have to do that on the separate pdb and CIF 
files and then merge the two or more CIF files into one if you have more than one ligand.  I must admit to this being 
theory I have not tested it in practice.

Best wishes
Nick
--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Prodrug bugs

[Nicholas Keep]

Dear CCP4
There is a bug in the ccp4i interface to prodrug on both linux and windows.
There is a title line that is read in to the command file which means the 
software does not run
Unrecognised keyword.
This can be removed using the run and view com file option
However on windows I then get the error Cannot find PRODRG data file 
(prodrg.param).
Turns out share/prodrg/prodrg.param is not bundled in the distribution
Works if I copy that over from linux.
Best wishes
Nick
--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Graduate Teaching Assistants- Birkbeck University of London

[Nicholas Keep]

There are two graduate teaching assistant available for October 2011 in the 
Dept of Biological
Sciences, Birkbeck University of London.  These positions require you to teach 
and support teaching
for up to 50% (17.5 hours a week) of your time during term and to undertake a Ph.D with a member of the academic staff. 
 Much of the teaching will be between 6 and 9pm as Birkbeck teaches mainly part-time students in the evening.  The post 
is not limited to UK or EU nationals,although you will be expected to teach in English.



The Dept of Biological Sciences at Birkbeck includes the well known 
Crystallography grouping which
has a history of protein crystallography going back to JD Bernal in the 1930s.
For a list of current dept members linking through to their research interests see 
http://www.bbk.ac.uk/biology/our-staff/academic


For applications and job details see 
https://www15.i-grasp.com/fe/tpl_birkbeckcollege01.asp?newms=jjid=40545;


--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Liquid nitrogen resistant flooring

[Nicholas Keep]

Can anyone recommend a floor coating that passes category 2 containment (ie not wood) that is resistant to liquid 
nitrogen.  Ie you can fill dewars on without cracking.  Various solutions our estates people have fitted have all proved 
unsatisfactory.

Bets wishes
Nick
--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Resolution and distance accuracies

[Nicholas keep]

We clearly have confidence in distance measurements in crystal 
structures of an order of magnitude better than the resolution ie 
0.1-0.3 Angstroms, but can anyone point me to a more exact theory of 
distance accuracy compared to optical resolution, preferably one that 
would apply to microscopy as well.

Have a Happy Christmas and see many of you at CCP4
Nick

[ccp4bb] [Fwd: [ccp4bb] Permanent X-ray Lab Manager Post London UK]

[Nicholas Keep]

There is just over a week left to apply for this X-Ray Lab Manager job in 
central London.
Best wishes
Nick
--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door
---BeginMessage---
Birkbeck College, University of London, has a long tradition in X-ray crystallography going back to JD Bernal.  As part 
of the Institute of Structural Molecular Biology with UCL we are looking for a permanent X-ray lab manager to be in 
charge of our new crystallisation facility (including imager on order), our recently purchased X-ray generator and 
detectors and to organise synchrotron time.  There will also be opportunities to carry out research in collaboration 
with the group leaders.


Informal enquiries can me made to Prof Gabriel Waksman g.waks...@mail.cryst.bbk.ac.uk 020 7631 6833 or myself (see below 
for contact details)


The formal details can be got from jobs.ac.uk
http://www.jobs.ac.uk/job/ABK630/x-ray-laboratory-manager-and-research-assistant/


The brief details are

X Ray Laboratory Manager and Research Assistant
Birkbeck College, University of London

Ref: 10419

We are seeking an experienced person to manage our protein X-ray crystallography laboratory and to provide research 
assistance to the Academic staff using the laboratory.


The successful candidate will train staff in the use of X-ray crystallographic equipment and software, and collaborate 
with academic staff and users on research projects that use the equipment. The newly refurbished laboratory has 
state-of-art equipment comprising an X-ray system, crystallisation robotics and imaging systems. The laboratory manager 
of this protein crystallography facility also co-ordinates applications for synchrotron time for X-ray data collection 
and helps users at these international facilities. At least three years previous experience in protein crystallography 
is essential.


Applicants should have a PhD, or equivalent experience.

Salary will be £33,669 rising to £38,568 per annum. Initial salary award will 
be dependent on skills and experience.


Closing date:  18 August 2010
Interview date: 2 September 2010

Birkbeck is an equal opportunities employer.




--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door
---End Message---

[ccp4bb] Graduate Teaching assistant/Phd Student Birkbeck University of London

[Nicholas Keep]

Birkbeck is recruiting a graduate teaching assistant to combine some teaching duties with doing a Ph.D. at one of the 
top centres for Structural biology in the UK.  The deadline for applications is 1st September to ideally start this 
October.  Please bring this to the attention of any suitable candidates you know of.
Further details can be found at 
http://jobs.bbk.ac.uk/fe/tpl_birkbeckcollege01.asp?s=hNwYvBGdQoFRwTtFoljobid=36208,9823722372key=9334034c=357661344056pagestamp=semstsgltmxwguvhpg

It is unlikely that this post will qualify for a work permit for applicants who 
are not EU nationals.


--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Permanent X-ray Lab Manager Post London UK

[Nicholas Keep]

Birkbeck College, University of London, has a long tradition in X-ray crystallography going back to JD Bernal.  As part 
of the Institute of Structural Molecular Biology with UCL we are looking for a permanent X-ray lab manager to be in 
charge of our new crystallisation facility (including imager on order), our recently purchased X-ray generator and 
detectors and to organise synchrotron time.  There will also be opportunities to carry out research in collaboration 
with the group leaders.


Informal enquiries can me made to Prof Gabriel Waksman g.waks...@mail.cryst.bbk.ac.uk 020 7631 6833 or myself (see below 
for contact details)


The formal details can be got from jobs.ac.uk
http://www.jobs.ac.uk/job/ABK630/x-ray-laboratory-manager-and-research-assistant/


The brief details are

X Ray Laboratory Manager and Research Assistant
Birkbeck College, University of London

Ref: 10419

We are seeking an experienced person to manage our protein X-ray crystallography laboratory and to provide research 
assistance to the Academic staff using the laboratory.


The successful candidate will train staff in the use of X-ray crystallographic equipment and software, and collaborate 
with academic staff and users on research projects that use the equipment. The newly refurbished laboratory has 
state-of-art equipment comprising an X-ray system, crystallisation robotics and imaging systems. The laboratory manager 
of this protein crystallography facility also co-ordinates applications for synchrotron time for X-ray data collection 
and helps users at these international facilities. At least three years previous experience in protein crystallography 
is essential.


Applicants should have a PhD, or equivalent experience.

Salary will be £33,669 rising to £38,568 per annum. Initial salary award will 
be dependent on skills and experience.


Closing date:  18 August 2010
Interview date: 2 September 2010

Birkbeck is an equal opportunities employer.




--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Processing to detector corners with XDS

[Nicholas Keep]

Sorry this is off topic.
I am trying to push a data set into the corners of the detectors as Mean I/SIGI looks strong for the circle that the 
XDS integrates to.  The resolution appears to be hard coded in the detector header (and is reported back by XDS in the 
.LP files) which seems to override any parameters I set in XDS.INP  ie defining resolution limits or setting outer limit 
to 0.0.


I have also integrated to the corners with imosflm so will try that data.

Best wishes
NIck

--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Thanks for the many responses

[Nicholas Keep]

Thanks for the many responses.  I had been setting the parameters right. The problem was I was not telling xds to go 
back as far as INIT in the reprocessing.  JOB ALL was the answer

Best wishes
Nick
--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] comparing coordinates- SUMMARY

[Nicholas Keep]

Thanks for the many emails I have received.  Particularly to Ed who wrote and posted a script to the board and other 
people who offered to do it over the weekend.


I have achieved what I want with the unsupported ccp4 program compar (Plea to CCP4 support- increase the array sizes by 
an order of magnitude or two in the distributed binaries- modern machines will be fine with this).  If you turn on 
monitoring of bad fits with a cut of 0.001  Angstrom then you get distance with every pair of atoms with the same name 
in the log file.  This can be extracted and imported into excel for ordering by size.


Most comparison programmes assume you want to move the structures to give the best fit before calculating the stats 
whereas I wanted not to move them to see the effect of the molecular replacement.  I also wanted the individual atom 
pairs not the average by residue etc.



The other responses are summarised below but I have not tested them.


Ed has posted his script to the  board.

Other suggestions- I have not tested these
-
you could you the distance matrix to compare two stricture.
In R there is a package bio3d that read the pdb's file and calculate the matrix.
http://www.r-project.org/
http://mccammon.ucsd.edu/~bgrant/bio3d/
-
Maybe Profit (http://www.bioinf.org.uk/software/) could be your friend ?
---
Looks like SSM should do that, just google on SSM
---
LSQMAN has a bunch of analysis and plot options. It always applies the current LSQ operator on one of the molecules, but 
as long as you don't do any superposition, that will be the identity operator.


http://xray.bmc.uu.se/usf/lsqman_man.html

-




--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Proportion of MR in the PDB

[Nicholas keep]

Does anyone have a good estimate of the proportion of molecular 
replacement structures in the PDB?
I tried using the search tools at RCSB and PDBe.  The PDBe gives 55.1% 
but apparently only 3411 structures have phase determination information 
recorded, so this does not look to be terribly comprehensive.

Thanks
Nick Keep

[ccp4bb] Group B factors in refmac

[Nicholas Keep]

We have been solving a protein complex at 3.1 A by molecular replacement. One 
copy of two chains in the asymmetric unit.
The two chains have fairly different average B factors.  As would be expected isotropic B factors in refmac overfits the 
data and leaves a large gap between R and Rfree.  TLS refinement with overall B factor gave a more reasonable separation 
of R and Rfree and more importantly more interpretable difference maps. Phenix. refine with TLS and group B factors 
bought the Rfree down further.  Refmac does not seem to have a group B factor option but I presume that by setting tight 
limits on the B factor constraints (I tried 0.1 on all of them (at most 1/10 of the defaults)- HAS ANYONE DONE ANY 
SYSTEMATIC WORK ON WHAT THIS SHOULD BE?) I think you effectively achieve two B factors per residue- main and side.  Is 
this correct?


Does anyone else have comments on Bfactor use at low resolution in refmac?
Best wishes
Nick

--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Postdoc Position in Electron Microscopy Birkbeck University of London

[Nicholas Keep]

PLEASE EMAIL h.sai...@mail.cryst.bbk.ac.uk NOT message poster


Dear Colleagues,

Two postdoctoral positions are available in the group of Professor Helen
Saibil, in the EM lab, Crystallography Department, Birkbeck College,
London. The posts are funded by a Wellcome Trust Programme grant in the
field of protein quality control, and will involve cryo EM studies on
chaperone-substrate interactions and on cellular aggregates, using both
single particle and tomography methods. The Birkbeck EM lab is well
equipped with a 300 kV Polara microscope, a 200 kV FEG system, and 120
kV and 100 kV cryo microscopes, as well as sample preparation equipment
for single particles, high pressure freezing, vitrified sections and
freeze substitution.
For further information, please see
http://people.cryst.bbk.ac.uk/~ubcg16z

Best wishes, Helen Saibil

[ccp4bb] Bucanneer and molecular replacement

[Nicholas Keep]

I have been trying to get my head around using bucanneer for molecular replacement.  I am not sure that I have 
understood the specify a heavy atom or MR model and what this does or the model to be extended options.


I am not sure of the difference between the two, and bucanneer will only run on certain models for reasons I do not 
understand.  With many input PDB files cbucanneer tends to crash with child process killed.


In fact I find that I can just read in the refmac map and the sequence and 
model building proceeds more or less as well.

I have donwloaded 1.3 from Kevin site (Linux) but this does not run at all
'bucaanneer-1st-correlation-mode takes logical got '

Thanks
Nick












--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6868  (Rosalind Franklin Laboratory)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] NCS restraints of domains

[Nicholas Keep]

I am refining a low (3A) resolution structure of a 3 domain protein. 
There are 4 copies in the ASU.  I have been applying tight NCS 
restraints by domain in refmac and have pulled the weak MR solution down 
to Rfree below 30 (just).


However my question is that in 2 of the 4 copies one of the domains is 
very poorly resolved.  I can lower Rfree by around 0.5% by omitting the 
domains from the PDB entirely or not applying the NCS restraints to 
these copies of the domain.  Clearly they are there and should resemble 
the moderately well resolved copies by coordinates but the way Bfactor 
restraints are applied between NCS copies seems to be the issue.  If 
tight restraints are included the B factors are much lower (30-40) 
rather than 60-80 for the poor domains.


I was wondering if there is a theoretically correct way to treat this?

Would applying TLS scaling to each domain lead to the residual B factors 
being more balanced?
Can a B factor offset be applied to the NCS restraints or could I only 
apply a coordinate restraint not a B factor restraint between certain 
copies?


Comments welcomed especially from Garib.

Happy New Year
Nick





--

Dr Nicholas H. Keep
Dean of Faculty of Science
Reader in Structural Biology
School of Crystallography,
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6868  (Rosalind Franklin Laboratory)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the 
crystallography entrance

and ring me or the department office from the internal phone by the door

[ccp4bb] Baubles (re imosflm)

[Nicholas Keep]

I have questions about baubles in general.  I find that using firefox
(3.0.4 windows) baubles logs do not open directly from ccp4i or imosflm
and I get an error i is not a registered protocol (or c) which I think
is the drive the file is on.  However if I open the file in via open
file then it works with graphs. This is true whether it is on the PC 
directly or on the network drive.


Internet explorer (7.0 windows) will open the files directly from ccp4i 
or imosflm but only displays the graphs if the log file is on my direct 
windows disks not on the drive that is shared between our PC and Linux 
networks.


Further what is recommended for 64 bit linux machines in terms of 
browser and jre as jre is only available in 32 bit I think. Do you 
reinstall firefox as a 32 bit version?


Comments/solutions welcomed.

best wishes
Nick


--

Dr Nicholas H. Keep
Dean of Faculty of Science
Reader in Structural Biology
School of Crystallography,
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email [EMAIL PROTECTED]
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6868  (Rosalind Franklin Laboratory)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the
crystallography entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Postdoctoral position in X-ray/EM at Birkbeck, University of London

[Nicholas Keep]

Contact [EMAIL PROTECTED] or [EMAIL PROTECTED]
for informal enquiries please do NOT reply to this email.

Postdoctoral Research Assistant – Ref: 10082

School of Crystallography, Faculty of Science

Full time, fixed term appointment for up to five years

The School of Crystallography/Institute of Structural and Molecular
Biology is seeking a Post-doctoral Research Assistant to carry out
structural analysis of complexes of bacterial type IV secretion systems
by cryo-electron microscopy.  This project is funded by a programme
grant from the Wellcome Trust to Prof Gabriel Waksman and is part of a
collaboration with Prof Helen Saibil. The successful candidate will join
the group of Prof Gabriel Waksman but will work in close collaboration
with the Saibil group to determine the cryo-EM structure of type IV
secretion sub-complexes. Further details on the research groups can be
found at http://people.cryst.bbk.ac.uk/~ubcg54a/  and
http://people.cryst.bbk.ac.uk/~ubcg16z/.

Applicants should have a PhD in Structural Molecular Biology, Biophysics
or a related area, postdoctoral research experience and relevant
research publications.

Salary range will be from £31,908 to £38,627 per annum inclusive of
London Allowance on Grade 7 or 8, initial salary will be dependent on
the skills and experience of the successful applicant.

Closing date for completed applications: 20 June 2008
Go to
https://www15.i-grasp.com/fe/tpl_birkbeckcollege01.asp?newms=jjid=24474;
to apply for this post.

If you have difficulties accessing this site please email,
[EMAIL PROTECTED], quoting the appropriate reference in the
subject header.

Birkbeck is an equal opportunities employer and encourages applications
from all candidates irrespective of gender, ethnicity, age, disability,
religious belief and sexual preference.

--

Dr Nicholas H. Keep
Dean of Faculty of Science
Reader in Structural Biology
School of Crystallography,
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email [EMAIL PROTECTED]
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6868  (Rosalind Franklin Laboratory)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the
crystallography entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Cis/trans double bonds in refmac/coot

[Nicholas Keep]

I have a structure with an unsaturated lipid in the active site, which 
according to the chemists has one cis and one trans double bond.  I 
would expect these to be controlled by the torsion angles in the cif 
files. However altering torsions between 0 and 180  makes no difference 
to the refinement and I get back what I put in terms of the fit of the 
molecule in coot.  Coot is great for fitting such molecules into the 
density, but you can flip the cis-trans fairly easily.


Is it correct that I just have to make sure the bonds are correct before 
starting refinement as the energy penalty for a cis/trans bond being 
wrong despite the torsion being set to a constant is simply too small?



Best wishes
Nick
--

Dr Nicholas H. Keep
Dean of Faculty of Science
Reader in Structural Biology
School of Crystallography,
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email [EMAIL PROTECTED]
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6868  (Rosalind Franklin Laboratory)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the 
crystallography entrance

and ring me or the department office from the internal phone by the door

Re: [ccp4bb] refmac5

[Nicholas Keep]

I think you get this problem whether or not you have selected to write a 
map.  I find that you need to open up the dialogue for maps set to 
temp.map and temp1.map and then the gui remembers that going forward 
whether or not you deselect the option to generate a map.  It also means 
you cannot run multiple refmac jobs without changing these output maps. 
 It is a feature which could be removed to advantage presumably the 
existence of the file names is checked whether or not they are needed.

Nick
--

Dr Nicholas H. Keep
Dean of Faculty of Science
Reader in Structural Biology
School of Crystallography,
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email [EMAIL PROTECTED]
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6868  (Rosalind Franklin Laboratory)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the 
crystallography entrance

and ring me or the department office from the internal phone by the door

[ccp4bb] X-ray lab manager Birkbeck University of London- permenant position

[Nicholas Keep]

Final reminder of this vacancy applications close in a week's time

X-ray Laboratory Manager  Research Assistant

We are seeking an experienced person to manage our protein X-ray
crystallography laboratory and to provide research assistance to the
Academic staff using the laboratory.

The successful candidate will train staff in the use of x-ray
crystallographic equipment and software, and collaborate with academic
staff users on research projects that use the equipment. The laboratory
has Rigaku generators and Mar image plates, it also has crystallisation
robots. The laboratory manager of this protein crystallography facility
also co-ordinates applications for synchrotron time for X-ray data
collection and helps users of these national facilities. At least three
years previous experience in protein crystallography is essential.

Applicants should have a PhD, or equivalent experience.

Salary will be £30,075 rising to £34,450 per annum. Initial salary award
will be dependent on skills and experience.

Download the job description and application form by visiting
http://www.bbk.ac.uk/hr/vacancies or email [EMAIL PROTECTED] for
an application pack.

Closing date for completed applications is midday 20th June 2007

Birkbeck is an equal opportunities employer.

--

Dr Nicholas H. Keep
Reader in Structural Biology
School of Crystallography,
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email [EMAIL PROTECTED]
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6868  (Rosalind Franklin Laboratory)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the
crystallography entrance
and ring me or the department office from the internal phone by the door

--

Dr Nicholas H. Keep
Reader in Structural Biology
School of Crystallography,
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email [EMAIL PROTECTED]
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6868  (Rosalind Franklin Laboratory)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the 
crystallography entrance

and ring me or the department office from the internal phone by the door

[ccp4bb] Crystallisation/Crystallography commercial permenant positions in Central London ONE WEEK TO APPLY

[Nicholas Keep]

There is just one week left to apply for these jobs
Structural Biologists (X-ray Crystallography)
Central London
(REF. SB0107)

Cancer Research Technology (CRT) is a specialist oncology company, which 
develops discoveries arising from Cancer Research UK and other 
prestigious oncology focused organisations’ research activities into 
potential therapies and diagnostics for the benefit of cancer patients.


CRT is seeking to recruit several structural biologists into its 
Discovery Laboratories, who will be responsible for the crystallisation 
and structure determination of pharmaceutically important protein-drug 
complexes.  The positions will be based within the Institute of 
Structural Molecular Biology (ISMB) at the School of Crystallography, 
Birkbeck College, adjacent to CRT’s Discovery Laboratories within the 
Wolfson Institute of Biomedical Research, UCL.   The School of 
Crystallography houses the ISMB Biophysics Centre, the ISMB Cryo-EM 
facility, and the ISMB X-ray Crystallography facility.


The successful candidates will have up to 5 years’ postdoctoral 
experience in structural biology within either academic or 
biopharmaceutical settings.  Experience of protein expression and 
purification, crystallisation, crystallographic data collection and 
structure solution and refinement methods are essential.  Previous 
involvement in projects relating to oncology would also be advantageous.


These are significant opportunities to influence the development of new 
cancer therapeutics and will suit highly talented individuals with 
strong interpersonal skills.  These are permanent positions with 
competitive salaries dependent upon experience and commensurate with 
their positions within CRT.


To apply for this position, please send two copies of your CV and a 
covering letter, quoting the relevant reference number, to the HR 
Manager, CRT, Sardinia House, Sardinia Street, London, WC2A 3NL or by 
email to [EMAIL PROTECTED]


No Agencies

Closing Date:  14th February 2007

We have a no smoking policy

CRT is an equal opportunities employer





--

Dr Nicholas H. Keep
Reader in Structural Biology
School of Crystallography,
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email [EMAIL PROTECTED]
Telephone 020-7631-6852  (Room G57 Office)
  020-7631-6868  (Rosalind Franklin Laboratory)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the 
crystallography entrance

and ring me or the department office from the internal phone by the door