Re: [ccp4bb] Refmac: removing selected ligand hydrogens after making a link

[James Holton]

After outputting the hydrogens, delete the ones you don't want and from 
then on do refinement with:


make hout Y
make hydr Y

When you do that, refmac will keep the hydrogens you put in, and also 
put them in the output.


-James Holton

MAD Scientist


On 3/29/2018 2:11 PM, Phil Jeffrey wrote:
I've got a couple of instances where I have non-standard amino acids, 
nevertheless present in the monomer dictionary, that have additional 
non-peptide covalent linkages.  I've figured out how to define these, 
but if I opt to output hydrogens as a diagnostic I see that Refmac 
doesn't delete the ligand hydrogens that were present at the linkage 
point.


Nothing catastrophic happens in refinement but extra atoms lying along 
other covalent bonds makes me a little queasy.


Is there something (non-obvious) in additional user-defined .cif 
library that I can use to do this ?  Do I simply define a new version 
of the monomer (w/o errant hydrogen) and hope that it overwrites the 
previous definition ?


I'm doing this at borderline atomic resolution.

Thanks
Phil Jeffrey
Princeton

[ccp4bb] Postdoctoral position in cell division at the Wellcome Centre for Cell Biology, Edinburgh, UK

[ARULANANDAM Jeyaprakash]

Dear All,

A Wellcome Trust funded postdoctoral position is available in our group 
(http://jeyaprakash.bio.ed.ac.uk) at the 
Wellcome Centre for Cell Biology (www.wcb.ed.ac.uk), 
University of Edinburgh to structurally characterise protein complexes involved 
in chromosome segregation during cell division, using a combination of cryoEM, 
SAXS and protein biochemistry.

Applicants must have a PhD (or will shortly be awarded a PhD) with training in 
biochemistry and structural biology. The successful candidate will be a highly 
motivated and enthusiastic individual with an outstanding academic track 
record, good communication skills and the ability to work as a team. Applicants 
with experience in single particle cryoEM and biochemistry are encouraged to 
apply.

The post is for 24 months in the first instance with a possibility of extension.

Closing Date: 30 March 2018

For further particulars and to apply for this post, please follow 
https://www.vacancies.ed.ac.uk/pls/corehrrecruit/erq_jobspec_version_4.jobspec?p_id=043008

Best wishes,
JP

Dr. A. Jeyaprakash Arulanandam
Wellcome Senior Research Fellow
Wellcome Centre for Cell Biology
University of Edinburgh
Michael Swann building (S5.18)
Max Born Crescent
Edinburgh EH9 3BF
UK
Tel: +44 131 6507113
Fax: +44 131 6080414
Web: http://jeyaprakash.bio.ed.ac.uk/
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[ccp4bb] Refmac: removing selected ligand hydrogens after making a link

[Phil Jeffrey]

I've got a couple of instances where I have non-standard amino acids, 
nevertheless present in the monomer dictionary, that have additional 
non-peptide covalent linkages.  I've figured out how to define these, 
but if I opt to output hydrogens as a diagnostic I see that Refmac 
doesn't delete the ligand hydrogens that were present at the linkage point.


Nothing catastrophic happens in refinement but extra atoms lying along 
other covalent bonds makes me a little queasy.


Is there something (non-obvious) in additional user-defined .cif library 
that I can use to do this ?  Do I simply define a new version of the 
monomer (w/o errant hydrogen) and hope that it overwrites the previous 
definition ?


I'm doing this at borderline atomic resolution.

Thanks
Phil Jeffrey
Princeton

Re: [ccp4bb] point group...321

[Eleanor Dodson]

Look at CCP4 v7.0 Program Documentation

reindexing

Yes PG 321 has two indexing options..


   - *i.e.* reindex (h,k,l) to (k,h,-l) which is equivalent here to
   reindexing (h,k,l) to (-h,-k,l).



On 29 March 2018 at 21:26, Gihan Ketawala  wrote:

> Hi,
> Can the point group 321 show indexing ambiguities? if not since I'm
> dealing with non-anomalous dataset can I use 3m1 instead?
>
> Thank you,
> Best,
> Gihan
>

Re: [ccp4bb] point group...321

[Keller, Jacob]

Yes, several, but it's only important when merging multiple data sets. And it's 
not really ambiguities but alternatives.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gihan 
Ketawala
Sent: Thursday, March 29, 2018 4:27 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] point group...321

Hi, 
Can the point group 321 show indexing ambiguities? if not since I'm dealing 
with non-anomalous dataset can I use 3m1 instead?

Thank you,
Best,
Gihan

[ccp4bb] point group...321

[Gihan Ketawala]

Hi, 
Can the point group 321 show indexing ambiguities? if not since I'm dealing 
with non-anomalous dataset can I use 3m1 instead?

Thank you,
Best,
Gihan

[ccp4bb] RA position in London

[Giulia Zanetti]

Dear all,

our lab is recruiting a research assistant to work on the COPII coat 
using biochemistry and structural cryo-EM.


The purpose of this job is to provide support to the group and assist 
research in the lab, and we are looking for an enthusiastic person who 
has experience in protein biochemistry.


We are based at the Institute of Structural and Molecular Biology, at 
Birkbeck College in London, within a vibrant and international research 
community, and with access to state-of-the-art cryo-EM equipment.


The job ad can be found at this link 
http://www.jobs.ac.uk/job/BIT470/research-assistant


Closing date is 27 April 2018, PhD not required.

Please do not hesitate to contact me to make any enquiries.

Thanks and all the best,

Giulia



Giulia Zanetti,

ISMB, Birkbeck

London WC1E 7HX

Re: [ccp4bb] A new capability on the STARANISO server: "PDBpeep"

[vincent Chaptal]

Dear Jacob and Gerard,

we performed a statistical analysis of anisotropy of the entire PDB, 
with a special focus on membrane proteins (Jacb, your other post).
You can find more details on this article: 
https://www.nature.com/articles/s41598-017-17216-1


We also performed an analysis by space group, not reported in the 
article, but not seeing anything coming out. The data used in the 
article is being reviewed at the moment to be available for you to play 
with. Hopefully, the reviewer is going to read your posts and is going 
to agree on the importance of analyzing this phenomenon.


all the best
Vincent

On 28/03/2018 20:35, Gerard Bricogne wrote:

Dear Jacob,

  Thank you for the appreciative comment.
  
  I am not sure that there is any such thing as an up-to-date

estimate of the prevalence of anisotropy in the PDB - but now you can
get a feel for it yourself by looking at any entries you want. However
please do not submit the whole PDB to the server - yet ;-) .

  From looking at anisotropy as visible through the overall scaling
Debye-Waller factor, I would say that whenever anisotropy is allowed
by the Laue group, it will be present, even if mild. Symmetry lower
than cubic means that intermolecular contacts along directions that
are not symmetry-equivalent will be different, and there is no reason
why different contacts should create identical degrees of long-range
order.


  Have fun!
  
   Gerard.


--
On Wed, Mar 28, 2018 at 06:13:29PM +, Keller, Jacob wrote:

Wow, this is really cool--just tried a quick look at a recent membrane protein 
(5eqi) and you can see right away that there is anisotropy.

I would guess this can be found in the literature, but how prevalent is 
anisotropy in the PDB?

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard 
Bricogne
Sent: Wednesday, March 28, 2018 11:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] A new capability on the STARANISO server: "PDBpeep"

Dear all,

  Ever since the WebGL viewer became available on the STARANISO server, we have found 
ourselves using it with increasing frequency to take a quick look (a "peep") at 
the diffraction data deposited with various PDB entries - for example, to try and 
identify a root cause for some sub-optimal refinement results, or, quite often, just out 
of sheer curiosity!

  This involved a totally straightforward procedure whereby the diffraction 
data file associated with a given PDB entry was downloaded from the PDB and 
subsequently uploaded to the STARANISO server.

  Gradually, however, this operation became so popular among some of us that we 
thought it would be useful to implement this simple procedure as an autonomous capability 
- and thus was born "PDBpeep" !

  You can access this new feature by connecting to

http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi

and enter a PDB code into the box. As indicated on that page, this provides 
only a cursory look at the overall quality of each dataset, and any further 
analysis or output can only be obtained by submitting the datafile to the 
STARANISO server. Better results would clearly be obtainable if the raw images 
for these datasets had been deposited and could be reprocessed, with the 
untruncated output of that processing then being submitted to the STARANISO 
server (reprocessing the images with autoPROC would combine those two steps 
into a single one).

  Most of the deposited datasets have been isotropically truncated, and 
their 3D view in WebGL often suggests that this truncation was too drastic. A 
number of entries will show infelicities - such as cusps and/or missing angular 
ranges, or even stripes caused by gaps between the modules of pixel detectors 
if the beam centre is at a position symmetric relative to those gaps - all 
marked up in blue.


  Our purpose in sharing this capability with the community is to bring a further 
contribution to the process of making everyone more "data quality aware" and 
keen to scrutinise more closely the protocols by which they collect diffraction data, or 
have such data collected on their behalf.


  We will be grateful to receive feedback about PDBpeep, just as we have 
been about the STARANISO server itself.

[ccp4bb] PhD studentship - Glasgow University/Astra Zeneca

[Laura Spagnolo]

Dear Colleagues,
Applications are invited for a PhD studentship position funded by the 
BBSRC-CASE scheme in the laboratory of Dr Laura Spagnolo, University of 
Glasgow, in collaboration with Dr Taiana Maia de Oliveira, Astra Zeneca, 
Cambridge. The project involves the cryo-electron microscopy study of large 
protein/nucleic acid complexes involved in the maintenance of genome stability.
Candidates should have a first or upper second class degree in biochemistry, 
cell biology or biological/medical science. The successful candidate will have 
the opportunity to work in both academic and industry setting during their 
studentship. The studentship is available to UK nationals and EU students who 
meet the UK residency requirements.
To apply, please send a CV and cover letter to 
laura.spagn...@glasgow.ac.uk. The closing 
date for applications is April 20th, 2018.
Best regards,
Laura



Dr Laura Spagnolo
Reader in Structural Biology
Institute of Molecular, Cell and Systems Biology
University of Glasgow
Room 409, Bower Building
University Avenue
Glasgow G12 8QQ
United Kingdom

Tel. + (0)141 3305133





[University of Glasgow: The Times Scottish University of the Year 2018]

[ccp4bb] Post-doc position at AstraZeneca

[Käck , Helena]

Dear all,

We have an opening for a Post-Doc Fellow in CryoEM/Structural biology at 
AstraZeneca in Gothenburg. The aim of the project is to study multi-protein 
complexes of relevance for cellular signaling. The project will be a 
collaboration with Dr. Alexey Amunts at SciLifeLab, Stockholm University.

For more information about the position and how to apply, follow this link:
https://job-search.astrazeneca.com/job/gothenburg/post-doc-fellow-cryoem-structural-biology-of-protein-complexes/7684/7417154

Kind regards,

Helena Käck


Dr Helena Käck
Associate Principal Scientist, Structure & Biophysics
__

AstraZeneca
R | Innovative Medicines | Discovery Sciences
Pepparedsleden 1, SE-432 83 Molndal Sweden R
helena.k...@astrazeneca.com
Tel +46 31 7064060

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Re: [ccp4bb] Are there reliable methods for Selenomet incorporation in Pichia ?

[HERMAN VAN TILBEURGH]

> 
> hi
> you can find details in this manuscript on how to label recombinant proteins 
> produced by P. pastoris
> Crystal structure of the effector AvrLm4-7 of Leptosphaeria maculans reveals 
> insights into its translocation into plant cells and recognition by 
> resistance proteins. 
> Blondeau K, Blaise F, Graille M, Kale SD, Linglin J, Ollivier B, Labarde A, 
> Lazar N, Daverdin G, Balesdent MH, Choi DH, Tyler BM, Rouxel T, van Tilbeurgh 
> H, Fudal I.
> 
> Plant J. 2015 Aug;83(4):610-24. doi: 10./tpj.12913. Epub 2015 Jul 14.
> 
> it is not easy to obtain a homogenous labeled sample, but if there are enough 
> methionines in you protein it might work
> all the best
> 
> 
> Herman van Tilbeurgh
> Professor structural biology
> Directeur Adjoint Ecole Doctorale Innovation Thérapeutique: du fondamental à 
> l'appliqué
> 
> Institut de Biologie Intégrative de la Cellule - I2BC
> UMR 9198 CNRS- Université Paris Sud
> Team: Fonction et Architecture des Assemblages MacroMoléculaires
> http://www.i2bc.paris-saclay.fr/spip.php?article256 
> 
> 
> Batiment 430
> 91405 Orsay
> France
> 
> Tel: 33 1 69 82 61 16
> herman.van-tilbeu...@u-psud.fr 
> 
> 
> 
> 
> 
>> Le 29 mars 2018 à 00:32, Anirban Banerjee > > a écrit :
>> 
>> Dear all,
>> 
>> There is not much by way of published literature on this. Are there 
>> unpublished methods that people have used and have found to work reliably ?
>> 
>> Any help will be very much appreciated.
>> 
>> Warm regards,
>> 
>> Anirban
>