Re: [ccp4bb] Eiger 16M detector in HKL2000

[Raghurama P Hegde]

Dear Aidong,

As Dr. Förster has rightly pointed out you need to have the latest version of 
HKL2000 to work with the HDF5 files from the Eiger detectors and as you must be 
aware the HKL2000 license should include use of Eiger detectors. We have 
recently used HKL2000 to process data from MASSIF-3 beamline at ESRF which uses 
a EIGER X 4M detector but we had to upgrade to the latest version of HKL2000.

With regards,
Raghu


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andreas 
Förster
Sent: Tuesday, December 19, 2017 11:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Eiger 16M detector in HKL2000

Dear Aidong,

as I don't have access to HKL2000 myself, I can't tell you what might need to 
be done to have the software display EIGER X 16M images.  Wladek showed me that 
it was possible.  It might just be a question of getting the latest version.

There are alternatives to HKL-2000.

DIALS can process EIGER data with no questions asked 
(https://dials.github.io/).  It is free, open-source software.  DIALS exists as 
a powerful command line tool but can also be run through the xia2 pipeline 
(https://xia2.github.io/).  Both are part of CCP4, but I'd recommend installing 
the latest DIALS nightly because development is rapid.  The developers respond 
quickly to questions.

XDS can process EIGER data 
(http://xds.mpimf-heidelberg.mpg.de/html_doc/XDS.html).  It is free to academic 
users.  To process data in HDF5 format (*.h5), make sure to download the neggia 
plugin (https://www.dectris.com/support/downloads/software/neggia, free, but 
registration required) and adjust the LIB= parameter to point to where the 
plugin is saved.  XDS is a command line tool, but several GUIs exist.

Please give DIALS or XDS a try and tell me how you get along.  If you continue 
to encounter problems, let me and the beamline staff at SSRF know.

All best.



Andreas



On Tue, Dec 19, 2017 at 6:48 AM, Aidong Han 
> wrote:
Hi All,

We have recently collected several data sets in the Shanghai synchrotron 
facility with a newly installed Eiger 16M. However, we are not able to process 
these data using our home HKL2000 package. Even though we can easily add this 
detector in, we can not display images. I believe ours has not been properly 
set up. While we are still waiting for a response from HKL2000 administration 
managers (it has been a few days), I wonder whether someone can provide me your 
solution since this detector has been in market for more than a year. Thank you 
for your help.

Sincerely,

Aidong

Re: [ccp4bb] 3D stereo and pymol

[Matic Kisovec]

Dear all,

in case anybody is interested in a used 3D setup for crystallography one is 
still available:
See here for more details: 
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg41144.html

Kind regards,
Matic.


On 12. 12. 2017 08:39, Jim Fairman wrote:
Reporting in a setup that we just made: Quadro P4000 + 3 pin stereo bracket + 
3d vision 2 kit + ASUS VG248QE.

Running System76's PoPOS Ubuntu 17.10 distro - you'll have to install a desktop 
environment that supports non-compositing (ie: XFCE).

Works beautifully.



--
Jim Fairman
C: 1-240-479-6575

On Tue, Nov 28, 2017 at 6:40 AM, mesters 
> wrote:
Hi,

yes, consumer cards do have OpenGL implemented on a chip but the Nvidia driver 
did not allow OpenGL 3D to work until February 2013. As of Nvidia driver 
version 314.07, Nvidia added OpenGL quad buffered 3D Stereo for GeForce cards 
(at least under MS Windows 7/8). However, this was never officially announced 
and officially supported and only works if the monitor is preset to run at 120 
Hz and the software automatically switches into full-screen mode. Sadly, 
windowed applications will not work. Under MS Windows 10, it does not seem to 
work anymore.

We have a monitor with a build in emitter and that one works with the 
smaller/cheaper Quadro cards without the 3-pin connector but, it is virtually 
impossible nowadays to get such a monitor in order to avoid needing to buy an 
expensive Nvidia card with a 3-pin connector.

To enjoy OpenGL quad buffered 3D Stereo, you will at least need a Quadro 
K4000/P4000/4000 with separate 3-pin bracket (all-in-all very expensive 
solution) or you will need to buy an older FX model such as the FX3700 with 
build-in 3-pin connector.

At the Bay in the USA, unused / brand-new FX3700s are being offered right now 
for about 90-110 US$. That's the cheapest way out and 512 MB memory is 
sufficient unless you are trying work with VERY big PDB files. If so, try to 
get your hands on a "new, see details" Quadro 4000 and a separate PNY 3-pin 
mini DIN stereo bracket (930-50764--000 C for about 20 US$) or a "new, see 
details" Quadro 5000 with build-in emitter.

Good luck

Jeroen.


Am 28.11.17 um 10:50 schrieb Johannes Cramer:
Hi Christine,

as far as I know, it does not work at all with Geforce cards. The Nvidia 
drivers do not support windowed quad buffered GL, which you need for 
coot/pymol. It does not matter whether you use Windows or Linux.
But this is based on my personal experience from around Oct. 2016. Maybe 
something changed quietly since then. Again, as far as I know, you need a 
Quadro card.

Cheers,
Johannes

2017-11-06 21:24 GMT+01:00 Christine Gee 
>:
Hi,

I have looked in the archive for posts about this, but there hasn't been one 
for about a year. Can anyone comment on whether they have managed to get a 
linux flavor and GeForce cards to work with pymol and/or coot 3D stereo? 
Geforce cards supposedly support openGL, but posts from October last year on 
the BB suggests that it only works in windows unless you have a monitor with a 
built in emitter. I would appreciate any feedback.

Regards
Christine




--
Dr. math. et dis. nat. Jeroen R. Mesters
Deputy, Senior Researcher & Lecturer
Program Coordinator Infection 
Biology

Institute of Biochemistry, University of Lübeck
Ratzeburger Allee 
160, 
23538 Lübeck, Germany
phone: +49-451-31013105 (secretariate -31013101)
fax: +49-451-31013104

[http://jobs.zeit.de/image-upload/logo_10564.jpg]
http://www.biochem.uni-luebeck.de
http://www.eine-stadt-sieht-gelb.de
http://www.uni-luebeck.de/studium/studiengaenge/infection-biology
http://www.iobcr.org
Visiting Professorship in Biophysics, University of South Bohemia (CZ)
President of the International Organization for Biological Crystallization 
(IOBCr)
--
If you can look into the seeds of time and tell which grain will grow and which 
will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act 
I, Scene 3)
--
"Aujourd'hui je sais qu'il n'y a pas de limites à la bêtise humaine - qu'elle 
est infinie." (Gustave Flaubert, French novelist, 1821-1880)
--
It is invariably the case that high resolution X-ray structures show 
significantly better agreement with solution observables such as coupling 
constants, 13C chemical shifts, and proton chemical shifts, than the 
corresponding NMR structures, including the very best ones. Hence, in most 
cases, a high-resolution crystal structure (< 2.0 Å) will provide a better 
description of the structure in solution than the corresponding NMR structure  
(Kuszewski, Gronenborn & Clore, 1996, Protein Science 5:1067-80)
--

Re: [ccp4bb] Eiger 16M detector in HKL2000

[Andreas Förster]

Dear Aidong,

as I don't have access to HKL2000 myself, I can't tell you what might need
to be done to have the software display EIGER X 16M images.  Wladek showed
me that it was possible.  It might just be a question of getting the latest
version.

There are alternatives to HKL-2000.

DIALS can process EIGER data with no questions asked (
https://dials.github.io/).  It is free, open-source software.  DIALS exists
as a powerful command line tool but can also be run through the xia2
pipeline (https://xia2.github.io/).  Both are part of CCP4, but I'd
recommend installing the latest DIALS nightly because development is
rapid.  The developers respond quickly to questions.

XDS can process EIGER data (
http://xds.mpimf-heidelberg.mpg.de/html_doc/XDS.html).  It is free to
academic users.  To process data in HDF5 format (*.h5), make sure to
download the neggia plugin (
https://www.dectris.com/support/downloads/software/neggia, free, but
registration required) and adjust the LIB= parameter to point to where the
plugin is saved.  XDS is a command line tool, but several GUIs exist.

Please give DIALS or XDS a try and tell me how you get along.  If you
continue to encounter problems, let me and the beamline staff at SSRF know.

All best.



Andreas



On Tue, Dec 19, 2017 at 6:48 AM, Aidong Han  wrote:

> Hi All,
>
> We have recently collected several data sets in the Shanghai synchrotron
> facility with a newly installed Eiger 16M. However, we are not able to
> process these data using our home HKL2000 package. Even though we can
> easily add this detector in, we can not display images. I believe ours has
> not been properly set up. While we are still waiting for a response from
> HKL2000 administration managers (it has been a few days), I wonder whether
> someone can provide me your solution since this detector has been in market
> for more than a year. Thank you for your help.
>
> Sincerely,
>
> Aidong
>
>




-- 

Andreas Förster, Ph.D.
MX Application Scientist, Scientific Sales
Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email:
andreas.foers...@dectris.com
DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
www.dectris.com

[image: LinkedIn] 
 [image: facebook]







Confidentiality Note: This message is intended only for the use of the
named
recipient(s) and may contain confidential and/or privileged information. If
you
are not the intended recipient, please contact the sender and delete the
message.
Any unauthorized use of the information contained in this message is
prohibited.

Re: [ccp4bb] Electron density map for publications

[raj kumar]

Thanks sir

On Tue, Dec 19, 2017 at 11:05 AM, Bernhard Rupp 
wrote:

> *Unbiased positive omit* difference density, not just any fo-fc.
>
> Br
>
> On Dec 18, 2017 9:22 PM, "chenzhonghao...@163.com" <
> chenzhonghao...@163.com> wrote:
>
> Dear Raj,
>
>   Usually,   fo-fc is the best way to show.
>
>
> best,
>
>
> --
> chenzhonghao...@163.com
>
>
> *From:* raj kumar 
> *Date:* 2017-12-19 13:07
> *To:* CCP4BB 
> *Subject:* [ccp4bb] Electron density map for publications
> Hi
> Which electron density map (fo-fc  or 2fo-fc) should I use for
> representing the density of the bound ligand?
> Thanks
> Raj
>
>
>

[ccp4bb] Eiger 16M detector in HKL2000

[Aidong Han]

Hi All,

We have recently collected several data sets in the Shanghai synchrotron 
facility with a newly installed Eiger 16M. However, we are not able to process 
these data using our home HKL2000 package. Even though we can easily add this 
detector in, we can not display images. I believe ours has not been properly 
set up. While we are still waiting for a response from HKL2000 administration 
managers (it has been a few days), I wonder whether someone can provide me your 
solution since this detector has been in market for more than a year. Thank you 
for your help.

Sincerely,

Aidong

  

Re: [ccp4bb] Electron density map for publications

[Bernhard Rupp]

*Unbiased positive omit* difference density, not just any fo-fc.

Br

On Dec 18, 2017 9:22 PM, "chenzhonghao...@163.com" 
wrote:

Dear Raj,

  Usually,   fo-fc is the best way to show.


best,


--
chenzhonghao...@163.com


*From:* raj kumar 
*Date:* 2017-12-19 13:07
*To:* CCP4BB 
*Subject:* [ccp4bb] Electron density map for publications
Hi
Which electron density map (fo-fc  or 2fo-fc) should I use for representing
the density of the bound ligand?
Thanks
Raj

Re: [ccp4bb] Electron density map for publications

[chenzhonghao...@163.com]

Dear Raj,

  Usually,   fo-fc is the best way to show.


best,




chenzhonghao...@163.com
 
From: raj kumar
Date: 2017-12-19 13:07
To: CCP4BB
Subject: [ccp4bb] Electron density map for publications
Hi
Which electron density map (fo-fc  or 2fo-fc) should I use for representing the 
density of the bound ligand?
Thanks
Raj

Re: [ccp4bb] Electron density map for publications

[Bernhard Rupp]

http://journals.iucr.org/d/issues/2013/02/00/index.html

 

Best, BR

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of raj kumar
Sent: Monday, December 18, 2017 8:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Electron density map for publications

 

Hi

Which electron density map (fo-fc  or 2fo-fc) should I use for representing the 
density of the bound ligand?

Thanks

Raj

[ccp4bb] Electron density map for publications

[raj kumar]

Hi
Which electron density map (fo-fc  or 2fo-fc) should I use for representing
the density of the bound ligand?
Thanks
Raj

Re: [ccp4bb] coordinate transformation

[James Holton]

Well, yes, a one-liner to move every atom to 1,1,1 would be:

awk '! /^ATOM|^HETAT/{print;next} {print substr($0,1,30) " 1.000   
1.000   1.000" substr($0,55)}' whatever.pdb > ref.pdb


Which I suppose is a bit of a long one-liner, but still only one line.  
The next line would be a call to "reforigin", or origins.com, using 
"ref.pdb" as the reference pdb file.  Many other useful one-liners can 
be found at DOI: 10.1002/spe.4380090403


Does that help?

-James Holton
MAD Scientist

On 12/18/2017 11:19 AM, Edward A. Berry wrote:

Neat idea!
And do you have a 1-line command for setting all the coordinates to 
1,1,1? or 0.1,0.1,0.1 if I still want it near the origin but biased 
toward the inside of the positive-going cell?

eab

On 12/14/2017 07:23 PM, James Holton wrote:
What I usually do for this is make a copy of the PDB file and change 
all the atom x-y-z positions to "1.000".  Then I use something like 
reforigin or my "origins.com" script to shift the original 
coordinates via allowed symmetry operations, origin shifts, or 
perhaps indexing ambiguities until it is as close as possible to the 
"reference", which is at 1,1,1.  I use 1,1,1 instead of 0,0,0 because 
there are generally at least two symmetry-equivalent places that are 
equidistant from the origin. Declaring the reference to be a bit 
off-center breaks that ambiguity, and also biases the result toward 
having all-positive x,y,z values.



In case it is interesting, my script is here:

http://bl831.als.lbl.gov/~jamesh/scripts/origins.com


You need to have the CCP4 suite set up for it to work.  Run it with 
no arguments to get instructions.



-James Holton

MAD Scientist


On 12/13/2017 5:50 AM, Kajander, Tommi A wrote:


Hello,

If someone could point this out would be very helpful... Wasnt there 
a simple script somewhere that would transfer coordinates close to 
origin - if they for some reason are not? Just cant find anything 
right away. Sure i have done this before...



Thanks,

Tommi

Re: [ccp4bb] Crystal structure of an unknown protein

[Kevin Jin]

HI Jiyong,

If you still have protein left, you may try to sequence it. In some cases,
even N-terminal digestion is very helpful. In my previous, I always got a
90KDa protein, which was very close to my target kinase. Based on the
protein sequencing, we identified it was one of those chaperones.

Best,

Kevin

On Sun, Dec 17, 2017 at 11:39 PM, Jiyong Su  wrote:

> Dear Pedro Matias,
>
> Thanks for you advice.
>
> After I manually changed the side chain of the residues, I got a
> "artificial" primary structure. I did a blast by using this primary
> structure.
> Finally, I found the amino acid sequence of this protein. The electron
> density could perfectly match the sequence.
> BTW, this protein is from a lovely weird bacteria which was cultured by a
> student.
>
> Best regards,
>
> Jiyong
>
>
>
>
> --
> Yours Sincerely,
>
> Jiyong Su
>
> The School of Life Sciences
> Northeast Normal University
> Changchun 130024, China
> Email: sujy...@nenu.edu.cn
> Tele: + 0086 13244318851
>
>
>
>
> 在 2017-12-14 21:08:57，Pedro Matias  写道：
> >Hello,
> >
> >Welcome to the club of unexpected results!
> >
> >You don't provide a lot of background, but based on what you wrote you can:
> >
> >1. Do a BLAST search using a known part of your sequence to find whether
> >this sequence has been deposited.
> >
> >2. Assign the different residues based on the chemical environment and
> >electron density and refine the structure.
> >
> >I'm sure you can submit the refined structure to the PDB even from an
> >unknown protein.
> >
> >Regards,
> >
> >Pedro Matias
> >
> >
> >Às 12:08 de 14/12/2017, Jiyong Su escreveu:
> >> Dear CCP4bb,
> >>
> >> In 2014, I collected a high quality data set from a crystal. But I
> >> could not solve the structure of that crystal because this protein is
> >> a contaminate.
> >> Recently, I used StruBE's Contaminer and fortunately got the solution.
> >> Thanks ContaMiner!!!  This protein is a contaminate protein.
> >>
> >> However, I found this protein is an unknown protein (about 180
> >> residues) whose amino acid sequence is not totally same as E.coli.
> >> There are about 20 point mutation sites comparing to the E.coli
> >> protein. This means this protein may be from an unknown bacteria.
> >>
> >> The space group of this crystal is new. There is also a new ligand in
> >> this protein.
> >>
> >> My question is how could I found the primary structure of this protein
> >> and how to deposit this protein in PDB.
> >>
> >> Best regards,
> >>
> >> Jiyong
> >>
> >
> >--
> >
> >Industry and Medicine Applied Crystallography
> >Macromolecular Crystallography Unit
> >___
> >Phones : (351-21) 446-9100 Ext. 1669
> > (351-21) 446-9669 (direct)
> > Fax   : (351-21) 441-1277 or 443-3644
> >
> >email : mat...@itqb.unl.pt
> >
> >http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
> >http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
> >
> >Mailing address :
> >Instituto de Tecnologia Quimica e Biologica António Xavier
> >Universidade Nova de Lisboa
> >Av. da República
> >2780-157 Oeiras
> >PORTUGAL
> >
> >ITQB NOVA, a great choice for your PhD
> >https://youtu.be/de6j-aaTWNQ
> >
> >Master Programme in Biochemistry for Health
> >https://youtu.be/UKstDCFjYI8
>
>
>


-- 
Kevin Jin

Sharing knowledge each other is always very joyful..

Website: http://www.jinkai.org/

[ccp4bb] Map transformation [was Re: [ccp4bb] coordinate transformation]

[Paul Emsley]

On 18/12/2017 13:15, Smith Liu wrote:

Dear All,

If I have a set of PDB with the corresponding density map, after I transform the PDB based on the suggestion 
of everybody, is any way to transform the map so that the map will be fit with the transformed PDB?




Seeing as no-one else has mentioned it..., you can do this with Coot: Extensions -> Map -> Transform map by 
LSQ model fit...


Or read the section 6.20 of the manual, titled "Map Transformation"

Paul.

[ccp4bb] Higher Scientific Officer positions available at The Institute of Cancer Research

[Rob Van Montfort]

The Institute of Cancer Research, London, is one of the world’s most 
influential cancer research institutes, with an outstanding record of 
achievement dating back more than 100 years. We provided the first convincing 
evidence that DNA damage is the basic cause of cancer, laying the foundation 
for the now universally accepted idea that cancer is a genetic disease. Today, 
The Institute of Cancer Research (ICR) leads the world at isolating 
cancer-related genes and discovering new targeted drugs for personalised cancer 
treatment. Under the leadership of our Chief Executive, Professor Paul Workman 
FRS, the ICR is ranked as the UK’s leading academic research centre. Together 
with our partner The Royal Marsden, we are rated in the top four cancer centres 
globally. The ICR is committed to attracting, developing and retaining the best 
minds in the world to join us in our mission – to make the discoveries that 
defeat cancer.
The Cancer Research UK Cancer Therapeutics Unit (CTU), within the Division of 
Cancer Therapeutics, is a multidisciplinary 'bench to bedside' centre, 
comprising around 160 staff dedicated to the discovery and development of novel 
therapeutics for the treatment of cancer. The Cancer Therapeutics Unit’s 
exciting goal is to discover high quality small molecule drug candidates and to 
progress these to clinical trial. All the scientific disciplines are in place 
to make this possible, including medicinal chemistry, biology, drug metabolism 
and clinical specialists who focus on new molecular targets emerging from human 
genome and ground breaking cell biology research.

Two Higher Scientific Officer position are now available in the Hit Discovery 
and Structural Design Team within the Unit. The team combines small-molecule 
high throughput screening, assay development and High-Throughput Screening with 
fragment-based hit discovery, biophysical assays and X-ray crystallography to 
enable structure-based drug design within the Unit. These methodologies are 
underpinned by state-of-the art protein expression, purification and 
characterisation capabilities, allowing for the generation of large quantities 
of high quality protein targets. Successful candidates will be integral members 
of a multidisciplinary project teams and will interact closely with the 
biologists, computational chemists, medicinal chemists and structural 
biologists.

One of the positions (ref 304) focusses on recombinant protein production for 
one of the cancer targets under study at the Unit. The successful candidate 
will be involved in performing the expression, purification and 
characterisation of one of our early stage drug targets, using contemporary 
expression systems and purification methods available within the Team. In 
addition, the post-holder is expected to characterise ligand and inhibitor 
binding to the recombinant proteins using biochemical and biophysical methods. 
Applicants must have a BSc in a biochemistry or related biological subject and 
in depth technical laboratory experience in protein expression and purification 
methodologies preferably related to drug discovery. Expertise in insect cell 
expression, assay development and/or knowledge of structural biology would be 
advantageous. The starting salary for the position will be in the range of 
£32,628 - £36,622 p.a. inclusive (based on previous experience) and the post is 
offered on a fixed term contract of 2 year. Informal enquiries to 
rob.vanmontf...@icr.ac.uk

The second position (ref 303) is in collaboration with the Cancer Biomarkers 
Team led by Prof. Johann de Bono. The successful candidate will use molecular 
and cell biology to develop cell-based assays for the screening of compound 
libraries and the profiling of cellular activities of inhibitors for a key 
cancer target. The post-holder is expected to apply detailed technical 
knowledge to develop, execute and analyse novel cell-based luciferase reporter 
assays for this target. Applicants must have a degree in Biochemistry, 
Molecular Biology or Cell biology and good technical laboratory experience in 
mammalian cell culture, molecular and cell biology methodologies is essential. 
Knowledge of reporter assays and drug discovery would be desirable. Appointment 
will be to a Higher Scientific Officer with starting salary in the range of 
£32,628 to £33,961 p.a. inclusive and the post is offered on a fixed term 
contract of 1 year in the first instance and benefits from a contributory 
defined benefit pension scheme and generous leave entitlement Informal 
enquiries to rosemary.bu...@icr.ac.uk or 
rob.vanmontf...@icr.ac.uk

The closing date for both positions is January 4th 2018.

Please DO NOT send your application to Dr van Montfort or Dr Burke, but see our 
website for more details and on how to apply: 
www.icr.ac.uk.

Dr. Rob van Montfort
Team Leader 

[ccp4bb] Scientist position in SM protein science - Biogen - #33174BR

[Rajesh Kumar Prakash]

Dear Colleagues,

We have an immediate job opening in our protein sciences group for a
molecular biologist/protein expression scientist (Application link and
details provided below). I would greatly appreciate if you can forward to
suitable candidates.

33174BR


Best regards,
Rajesh Kumar Prakash



Scientist I, Small Molecule Protein Science

US-MA-Cambridge

*Summary*

The Physical Biochemistry department is seeking an independent and highly
motivated Molecular Biologist to join the Small Molecule Protein Sciences
group (SMPS) at the Scientist I level. The SMPS is responsible for
providing high quality protein reagents for small molecule targets to the
Bioassays, Biophysics and the Structural biology groups.


Job Description

The Physical Biochemistry department is seeking an independent and highly
motivated Molecular Biologist to join the Small Molecule Protein Sciences
group (SMPS) at the Scientist I level. The SMPS is responsible for
providing high quality protein reagents for small molecule targets to the
Bioassays, Biophysics and the Structural biology groups. The successful
candidate must possess a broad set of skills, including Molecular Biology
and expression of proteins from bacterial and eukaryotic hosts. Special
emphasis will be given to candidates with the ability to carry out rapid
construct designs and purification. The selected individual will have the
opportunity to work in cross-functional teams and should be able to clearly
communicate their results and accomplishments to a broad audience at team
meetings and in written reports.

*Qualifications*

• The selected candidate should exhibit expertise in Molecular Biology,
including a variety of modern cloning approaches, construct design,
sequence bioinformatics and tagging strategies.
• The ideal candidate would have experience expressing IMP (channels,
transporters, GPCRs) expression strategies from multiple hosts.
• The candidate should have demonstrated by publications or other means, an
ability to carry out a variety of construct designs, expression strategies
and usage of multiple hosts. In addition, a sound knowledge of downstream
small and large scale purification will be highly valued.
• Good experience in parallel, high throughput approaches to cloning and
small scale expression will be necessary.
• Working knowledge of Akta or equivalent instruments will be considered an
asset.
• Bioinformatics programming (PERL, PYTHON) to decipher protein domains,
sequence and structural alignments will be considered an asset.
• This candidate will also work with external CROs to coordinate molecular
biology, expression and purification handoffs.
• Must be adept at following protocols and should have the scientific
experience to modify them when the situation arises.
• The candidate should have excellent verbal and written communication
skills. Clear scientific presentation skills at project and team meetings
are a must.
• Must be excellent in organization skills. The candidate is expected to
document all aspects of the experiments performed and be able to conduct
independent research to collect and archive all necessary information from
the literature.
• Demonstration of innovative approaches to problem solving is essential.

*Education*

Ph.D in Molecular Biology, Biochemistry or other suitable discipline.

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

[Edward A. Berry]

This is something you would normally not do in the course of refining a protein 
structure, because the structure would no longer correspond to the observed 
structure factors and no longer be consistent with the symops of the particular 
space group.

There are applications for it in multi-crystal averaging, or to compare 
directly the density map for structures from non-isomorphous crystals. For 
doing this it is important to understand the difference between a MAP file 
(.map, .ccp4) and a DATA file (.mtz). There are programs for 
rotating/translating electron density (from a map file) given the 
rotation-translation operator. I think ccp4 mapmask(?), also the uppsala RAVE 
and MAVE packages.
So you could generate a map from your mtz (ccp4 prog fft), get the operator 
relating new position to old
 (coot or LSQAB? or LSQMAN), transform ("skew") the map to the new location in 
a p1 cell, and calculate new p1 phased structure factors with SFALL (or use the map file 
directly in coot).  You need a mask for the skew operation, you can make it from your 
coordinates using mapmask or RAVE mama.
 
On 12/18/2017 10:40 AM, Smith Liu wrote:

sorry, how i move the mtz into the transformed pdb for the question in my 
previous email?




Smith Liu
邮箱：smith_liu...@163.com



签名由 网易邮箱大师  定制



在2017年12月18日 23:37，Smith Liu  写道：
thanks. i may mean something other. for example, if i rotate the pdb by 30 
degree (or 29.5 degree), or i shift the pdb along x-axis by something for 
example 0.123*a, then how i move the mtz map correspondingly for the fitting of 
mtz into the transformed map?




Smith Liu
邮箱：smith_liu...@163.com




签名由 网易邮箱大师  定制



在2017年12月18日 21:58，herman.schreu...@sanofi.com 
 写道：

Dear Smith,

The map extends through the whole crystal. What happens is that the map 
is calculated around the atom you clicked on during centering. So by centering 
on your transformed pdb, you will sample the same map at a different position. 
Just load your transformed pdb and untransformed mtz and try.

If the transformed pdb does not fit the map, something went wrong 
during the transformation of your pdb. If you have applied an origin shift (is 
not equal to applying a crystallographic symmetry operation), you have to 
recalculate the mtz, e.g. by running another round of refinement.

I hope this is clear so.

Herman

*Von:*Smith Liu [mailto:smith_liu...@163.com 
]
*Gesendet:* Montag, 18. Dezember 2017 14:52
*An:*Schreuder, Herman /DE
*Betreff:* [EXTERNAL] Re: [ccp4bb] AW: Re: [ccp4bb] coordinate 
transformation

you mean the mtz map will transform simutaneously?




*Smith Liu*

邮箱：smith_liu...@163.com 

签名由网易邮箱大师 

 定制




在2017年12月18日 21:26，herman.schreu...@sanofi.com 
 写道：

If you use coot with on the fly map calculation (e.g. you load an mtz 
and not a map file), you do not need to transform the map. Otherwise I would 
recommend to run one more round of refinement and produce a new map your usual 
way. This will also get rid of any rounding errors due to the transformation.

Best,

Herman

*Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK 
] *Im Auftrag von *Smith Liu
*Gesendet:* Montag, 18. Dezember 2017 14:16
*An:* CCP4BB@JISCMAIL.AC.UK 
*Betreff:* [EXTERNAL] Re: [ccp4bb] coordinate transformation

Dear All,

If I have a set of PDB with the corresponding density map, after I 
transform the PDB based on the suggestion of everybody, is any way to transform 
the map so that the map will be fit with the transformed PDB?

Smith




At 2017-12-18 18:39:34, "Eleanor Dodson" 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk 
> wrote:

I 

Re: [ccp4bb] coordinate transformation

[Edward A. Berry]

On 12/18/2017 05:39 AM, Eleanor Dodson wrote:

I showed you pdbset ..
Find the centre of mass for your assembly.
Move it where you will


Thanks. What James was suggesting was somewhat different (if I understood 
correctly): move EVERY ATOM to 1,1,1.
like:
  awk -v  FIELDWIDTHS="30 24 26" \
  '$1~/ATOM|HETATM/ && $2="   1.000   1.000   1.000" {print $1 $2 $3}' \
  3AEF.pdb
Then his origins program will find the symop/origin transform that moves the 
protein closest to that point. But come to think of it, moving COM to that 
point would probably have the same effect. Need to think about a lop-sided 
2-domain protein, where the symop is going to switch the orientation of 
large/small domains, and the large domain is negative of the com putting it 
outside the cell. but the com will be offset into the large domain, so probably 
still ok.

ORIGINS does assume like atoms have the same chain/resno in the different 
structures, which is not the case for 3AEF and friends, but they are close 
enough that it gives the right answer anyway.


pdbset xyzin mow.pdb
end
Find  CoM 0.7 1.3 -0.2

Hmm - a little thought - centre at 1 -1 0   say

pdbset yzin now.pdb xyzout changed.pdb

symgen x , y-2, z

end

New CoM  0.7 -0.7  -0.2

Eleanor





On 18 December 2017 at 00:19, Edward A. Berry > wrote:

Neat idea!
And do you have a 1-line command for setting all the coordinates to 1,1,1? 
or 0.1,0.1,0.1 if I still want it near the origin but biased toward the inside 
of the positive-going cell?
eab


On 12/14/2017 07:23 PM, James Holton wrote:

What I usually do for this is make a copy of the PDB file and change all the atom x-y-z positions to 
"1.000".  Then I use something like reforigin or my "origins.com " 
script to shift the original coordinates via allowed symmetry operations, origin shifts, or perhaps indexing 
ambiguities until it is as close as possible to the "reference", which is at 1,1,1.  I use 1,1,1 instead 
of 0,0,0 because there are generally at least two symmetry-equivalent places that are equidistant from the origin. 
Declaring the reference to be a bit off-center breaks that ambiguity, and also biases the result toward having 
all-positive x,y,z values.


In case it is interesting, my script is here:

http://bl831.als.lbl.gov/~jamesh/scripts/origins.com 



You need to have the CCP4 suite set up for it to work.  Run it with no 
arguments to get instructions.


-James Holton

MAD Scientist


On 12/13/2017 5:50 AM, Kajander, Tommi A wrote:


Hello,

If someone could point this out would be very helpful... Wasnt 
there a simple script somewhere that would transfer coordinates close to origin 
- if they for some reason are not? Just cant find anything right away. Sure i 
have done this before...


Thanks,

Tommi

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

[Tristan Croll]

Assuming you have a good reason for doing that, I'd suggest the best 
approach would be to first generate a real-space map covering your 
original coordinates, and then apply the transform to that. To transform 
a volumetric map, all you're actually transforming is the (x,y,z) 
coordinate of its origin and the three vectors defining its axes - but I 
must confess I don't know off the top of my head any GUI tools to do 
that for you. Chimera can almost certainly do it, if you look through 
the manual.


On 2017-12-18 15:37, Smith Liu wrote:

thanks. i may mean something other. for example, if i rotate the pdb
by 30 degree (or 29.5 degree), or i shift the pdb along x-axis by
something for example 0.123*a, then how i move the mtz map
correspondingly for the fitting of mtz into the transformed map?

Smith Liu

邮箱：smith_liu...@163.com

签名由 网易邮箱大师 [4] 定制


在2017年12月18日 21:58，herman.schreu...@sanofi.com 写道：

Dear Smith,

The map extends through the whole crystal. What happens is that the
map is calculated around the atom you clicked on during centering.
So by centering on your transformed pdb, you will sample the same
map at a different position. Just load your transformed pdb and
untransformed mtz and try.

If the transformed pdb does not fit the map, something went wrong
during the transformation of your pdb. If you have applied an origin
shift (is not equal to applying a crystallographic symmetry
operation), you have to recalculate the mtz, e.g. by running another
round of refinement.

I hope this is clear so.

Herman

VON: Smith Liu [mailto:smith_liu...@163.com]
GESENDET: Montag, 18. Dezember 2017 14:52
AN: Schreuder, Herman /DE
BETREFF: [EXTERNAL] Re: [ccp4bb] AW: Re: [ccp4bb] coordinate
transformation

you mean the mtz map will transform simutaneously?

SMITH LIU

邮箱：smith_liu...@163.com

签名由 网易邮箱大师 [1] 定制

在2017年12月18日 21:26，herman.schreu...@sanofi.com 写道：

If you use coot with on the fly map calculation (e.g. you load an
mtz and not a map file), you do not need to transform the map.
Otherwise I would recommend to run one more round of refinement and
produce a new map your usual way. This will also get rid of any
rounding errors due to the transformation.

Best,

Herman

VON: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] IM AUFTRAG
VON Smith Liu
GESENDET: Montag, 18. Dezember 2017 14:16
AN: CCP4BB@JISCMAIL.AC.UK
BETREFF: [EXTERNAL] Re: [ccp4bb] coordinate transformation

Dear All,

If I have a set of PDB with the corresponding density map, after I
transform the PDB based on the suggestion of everybody, is any way
to transform the map so that the map will be fit with the
transformed PDB?

Smith

At 2017-12-18 18:39:34, "Eleanor Dodson"
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

I showed you pdbset ..

Find the centre of mass for your assembly.

Move it where you will

pdbset xyzin mow.pdb

end

Find CoM 0.7 1.3 -0.2

Hmm - a little thought - centre at 1 -1 0 say

pdbset yzin now.pdb xyzout changed.pdb

symgen x , y-2, z

end

New CoM 0.7 -0.7 -0.2

Eleanor

On 18 December 2017 at 00:19, Edward A. Berry 
wrote:

Neat idea!
And do you have a 1-line command for setting all the coordinates to
1,1,1? or 0.1,0.1,0.1 if I still want it near the origin but biased
toward the inside of the positive-going cell?
eab

On 12/14/2017 07:23 PM, James Holton wrote:

What I usually do for this is make a copy of the PDB file and change
all the atom x-y-z positions to "1.000". Then I use something like
reforigin or my "origins.com [2]" script to shift the original
coordinates via allowed symmetry operations, origin shifts, or
perhaps indexing ambiguities until it is as close as possible to the
"reference", which is at 1,1,1. I use 1,1,1 instead of 0,0,0 because
there are generally at least two symmetry-equivalent places that are
equidistant from the origin. Declaring the reference to be a bit
off-center breaks that ambiguity, and also biases the result toward
having all-positive x,y,z values.

In case it is interesting, my script is here:

http://bl831.als.lbl.gov/~jamesh/scripts/origins.com [3]

You need to have the CCP4 suite set up for it to work. Run it with
no arguments to get instructions.

-James Holton

MAD Scientist

On 12/13/2017 5:50 AM, Kajander, Tommi A wrote:

Hello,

If someone could point this out would be very helpful... Wasnt
there a simple script somewhere that would transfer coordinates
close to origin - if they for some reason are not? Just cant find
anything right away. Sure i have done this before...

Thanks,

Tommi



Links:
--
[1]
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.163.com_dashi_dlpro.html-3Ffrom-3Dmail88d=DwMGbwc=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPor=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQm=VsiJhHbT-qp6n3QHdvilZeqY-0tA4mSqlVkx6nStzhMs=0Zu9ZB12d-Kh3exqmmGcW7PZIzCGKTXlXat7Qffx-lke=
[2]

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

[Smith Liu]

sorry, how i move the mtz into the transformed pdb for the question in my 
previous email?




| |
Smith Liu
|
|
邮箱：smith_liu...@163.com
|

签名由 网易邮箱大师 定制




在2017年12月18日 23:37，Smith Liu 写道：
thanks. i may mean something other. for example, if i rotate the pdb by 30 
degree (or 29.5 degree), or i shift the pdb along x-axis by something for 
example 0.123*a, then how i move the mtz map correspondingly for the fitting of 
mtz into the transformed map?




| |
Smith Liu
|
|
邮箱：smith_liu...@163.com
|

签名由 网易邮箱大师 定制




在2017年12月18日 21:58，herman.schreu...@sanofi.com 写道：

Dear Smith,

The map extends through the whole crystal. What happens is that the map is 
calculated around the atom you clicked on during centering. So by centering on 
your transformed pdb, you will sample the same map at a different position. 
Just load your transformed pdb and untransformed mtz and try.

If the transformed pdb does not fit the map, something went wrong during the 
transformation of your pdb. If you have applied an origin shift (is not equal 
to applying a crystallographic symmetry operation), you have to recalculate the 
mtz, e.g. by running another round of refinement.

I hope this is clear so.

Herman

 

Von: Smith Liu [mailto:smith_liu...@163.com]
Gesendet: Montag, 18. Dezember 2017 14:52
An: Schreuder, Herman /DE
Betreff: [EXTERNAL] Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

 

you mean the mtz map will transform simutaneously?




|

|

Smith Liu

|
|

邮箱：smith_liu...@163.com

|

签名由 网易邮箱大师 定制






在2017年12月18日 21:26，herman.schreu...@sanofi.com写道：

If you use coot with on the fly map calculation (e.g. you load an mtz and not a 
map file), you do not need to transform the map. Otherwise I would recommend to 
run one more round of refinement and produce a new map your usual way. This 
will also get rid of any rounding errors due to the transformation.

 

Best,

Herman

 

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Smith Liu
Gesendet: Montag, 18. Dezember 2017 14:16
An:CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] coordinate transformation

 

Dear All,

 

If I have a set of PDB with the corresponding density map, after I transform 
the PDB based on the suggestion of everybody, is any way to transform the map 
so that the map will be fit with the transformed PDB?

 

Smith






At 2017-12-18 18:39:34, "Eleanor Dodson" 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

I showed you pdbset ..

Find the centre of mass for your assembly.

Move it where you will

pdbset xyzin mow.pdb

end

Find  CoM 0.7 1.3 -0.2

Hmm - a little thought - centre at 1 -1 0   say

pdbset yzin now.pdb xyzout changed.pdb

symgen x , y-2, z 

end

New CoM  0.7 -0.7  -0.2

Eleanor

 

 

 

On 18 December 2017 at 00:19, Edward A. Berry  wrote:

Neat idea!
And do you have a 1-line command for setting all the coordinates to 1,1,1? or 
0.1,0.1,0.1 if I still want it near the origin but biased toward the inside of 
the positive-going cell?
eab



On 12/14/2017 07:23 PM, James Holton wrote:

What I usually do for this is make a copy of the PDB file and change all the 
atom x-y-z positions to "1.000".  Then I use something like reforigin or my 
"origins.com" script to shift the original coordinates via allowed symmetry 
operations, origin shifts, or perhaps indexing ambiguities until it is as close 
as possible to the "reference", which is at 1,1,1.  I use 1,1,1 instead of 
0,0,0 because there are generally at least two symmetry-equivalent places that 
are equidistant from the origin. Declaring the reference to be a bit off-center 
breaks that ambiguity, and also biases the result toward having all-positive 
x,y,z values.


In case it is interesting, my script is here:

http://bl831.als.lbl.gov/~jamesh/scripts/origins.com


You need to have the CCP4 suite set up for it to work.  Run it with no 
arguments to get instructions.


-James Holton

MAD Scientist


On 12/13/2017 5:50 AM, Kajander, Tommi A wrote:


Hello,

If someone could point this out would be very helpful... Wasnt there a simple 
script somewhere that would transfer coordinates close to origin - if they for 
some reason are not? Just cant find anything right away. Sure i have done this 
before...


Thanks,

Tommi

 

 

 

 

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

[Smith Liu]

thanks. i may mean something other. for example, if i rotate the pdb by 30 
degree (or 29.5 degree), or i shift the pdb along x-axis by something for 
example 0.123*a, then how i move the mtz map correspondingly for the fitting of 
mtz into the transformed map?




| |
Smith Liu
|
|
邮箱：smith_liu...@163.com
|

签名由 网易邮箱大师 定制




在2017年12月18日 21:58，herman.schreu...@sanofi.com 写道：

Dear Smith,

The map extends through the whole crystal. What happens is that the map is 
calculated around the atom you clicked on during centering. So by centering on 
your transformed pdb, you will sample the same map at a different position. 
Just load your transformed pdb and untransformed mtz and try.

If the transformed pdb does not fit the map, something went wrong during the 
transformation of your pdb. If you have applied an origin shift (is not equal 
to applying a crystallographic symmetry operation), you have to recalculate the 
mtz, e.g. by running another round of refinement.

I hope this is clear so.

Herman

 

Von: Smith Liu [mailto:smith_liu...@163.com]
Gesendet: Montag, 18. Dezember 2017 14:52
An: Schreuder, Herman /DE
Betreff: [EXTERNAL] Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

 

you mean the mtz map will transform simutaneously?




|

|

Smith Liu

|
|

邮箱：smith_liu...@163.com

|

签名由 网易邮箱大师 定制






在2017年12月18日 21:26，herman.schreu...@sanofi.com写道：

If you use coot with on the fly map calculation (e.g. you load an mtz and not a 
map file), you do not need to transform the map. Otherwise I would recommend to 
run one more round of refinement and produce a new map your usual way. This 
will also get rid of any rounding errors due to the transformation.

 

Best,

Herman

 

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Smith Liu
Gesendet: Montag, 18. Dezember 2017 14:16
An:CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] coordinate transformation

 

Dear All,

 

If I have a set of PDB with the corresponding density map, after I transform 
the PDB based on the suggestion of everybody, is any way to transform the map 
so that the map will be fit with the transformed PDB?

 

Smith






At 2017-12-18 18:39:34, "Eleanor Dodson" 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

I showed you pdbset ..

Find the centre of mass for your assembly.

Move it where you will

pdbset xyzin mow.pdb

end

Find  CoM 0.7 1.3 -0.2

Hmm - a little thought - centre at 1 -1 0   say

pdbset yzin now.pdb xyzout changed.pdb

symgen x , y-2, z 

end

New CoM  0.7 -0.7  -0.2

Eleanor

 

 

 

On 18 December 2017 at 00:19, Edward A. Berry  wrote:

Neat idea!
And do you have a 1-line command for setting all the coordinates to 1,1,1? or 
0.1,0.1,0.1 if I still want it near the origin but biased toward the inside of 
the positive-going cell?
eab



On 12/14/2017 07:23 PM, James Holton wrote:

What I usually do for this is make a copy of the PDB file and change all the 
atom x-y-z positions to "1.000".  Then I use something like reforigin or my 
"origins.com" script to shift the original coordinates via allowed symmetry 
operations, origin shifts, or perhaps indexing ambiguities until it is as close 
as possible to the "reference", which is at 1,1,1.  I use 1,1,1 instead of 
0,0,0 because there are generally at least two symmetry-equivalent places that 
are equidistant from the origin. Declaring the reference to be a bit off-center 
breaks that ambiguity, and also biases the result toward having all-positive 
x,y,z values.


In case it is interesting, my script is here:

http://bl831.als.lbl.gov/~jamesh/scripts/origins.com


You need to have the CCP4 suite set up for it to work.  Run it with no 
arguments to get instructions.


-James Holton

MAD Scientist


On 12/13/2017 5:50 AM, Kajander, Tommi A wrote:


Hello,

If someone could point this out would be very helpful... Wasnt there a simple 
script somewhere that would transfer coordinates close to origin - if they for 
some reason are not? Just cant find anything right away. Sure i have done this 
before...


Thanks,

Tommi

 

 

 

 

[ccp4bb] AW: Re: [ccp4bb] coordinate transformation

[Herman . Schreuder]

If you use coot with on the fly map calculation (e.g. you load an mtz and not a 
map file), you do not need to transform the map. Otherwise I would recommend to 
run one more round of refinement and produce a new map your usual way. This 
will also get rid of any rounding errors due to the transformation.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Smith Liu
Gesendet: Montag, 18. Dezember 2017 14:16
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] coordinate transformation

Dear All,

If I have a set of PDB with the corresponding density map, after I transform 
the PDB based on the suggestion of everybody, is any way to transform the map 
so that the map will be fit with the transformed PDB?

Smith




At 2017-12-18 18:39:34, "Eleanor Dodson" 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:

I showed you pdbset ..
Find the centre of mass for your assembly.
Move it where you will
pdbset xyzin mow.pdb
end
Find  CoM 0.7 1.3 -0.2
Hmm - a little thought - centre at 1 -1 0   say
pdbset yzin now.pdb xyzout changed.pdb
symgen x , y-2, z
end
New CoM  0.7 -0.7  -0.2
Eleanor



On 18 December 2017 at 00:19, Edward A. Berry 
> wrote:
Neat idea!
And do you have a 1-line command for setting all the coordinates to 1,1,1? or 
0.1,0.1,0.1 if I still want it near the origin but biased toward the inside of 
the positive-going cell?
eab


On 12/14/2017 07:23 PM, James Holton wrote:
What I usually do for this is make a copy of the PDB file and change all the 
atom x-y-z positions to "1.000".  Then I use something like reforigin or my 
"origins.com"
 script to shift the original coordinates via allowed symmetry operations, 
origin shifts, or perhaps indexing ambiguities until it is as close as possible 
to the "reference", which is at 1,1,1.  I use 1,1,1 instead of 0,0,0 because 
there are generally at least two symmetry-equivalent places that are 
equidistant from the origin. Declaring the reference to be a bit off-center 
breaks that ambiguity, and also biases the result toward having all-positive 
x,y,z values.


In case it is interesting, my script is here:

http://bl831.als.lbl.gov/~jamesh/scripts/origins.com


You need to have the CCP4 suite set up for it to work.  Run it with no 
arguments to get instructions.


-James Holton

MAD Scientist


On 12/13/2017 5:50 AM, Kajander, Tommi A wrote:

Hello,

If someone could point this out would be very helpful... Wasnt there a simple 
script somewhere that would transfer coordinates close to origin - if they for 
some reason are not? Just cant find anything right away. Sure i have done this 
before...


Thanks,

Tommi

Re: [ccp4bb] coordinate transformation

[Smith Liu]

Dear All,


If I have a set of PDB with the corresponding density map, after I transform 
the PDB based on the suggestion of everybody, is any way to transform the map 
so that the map will be fit with the transformed PDB?


Smith







At 2017-12-18 18:39:34, "Eleanor Dodson" 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

I showed you pdbset ..

Find the centre of mass for your assembly.

Move it where you will


pdbset xyzin mow.pdb

end

Find  CoM 0.7 1.3 -0.2


Hmm - a little thought - centre at 1 -1 0   say


pdbset yzin now.pdb xyzout changed.pdb


symgen x , y-2, z 


end


New CoM  0.7 -0.7  -0.2


Eleanor









On 18 December 2017 at 00:19, Edward A. Berry  wrote:
Neat idea!
And do you have a 1-line command for setting all the coordinates to 1,1,1? or 
0.1,0.1,0.1 if I still want it near the origin but biased toward the inside of 
the positive-going cell?
eab


On 12/14/2017 07:23 PM, James Holton wrote:
What I usually do for this is make a copy of the PDB file and change all the 
atom x-y-z positions to "1.000".  Then I use something like reforigin or my 
"origins.com" script to shift the original coordinates via allowed symmetry 
operations, origin shifts, or perhaps indexing ambiguities until it is as close 
as possible to the "reference", which is at 1,1,1.  I use 1,1,1 instead of 
0,0,0 because there are generally at least two symmetry-equivalent places that 
are equidistant from the origin. Declaring the reference to be a bit off-center 
breaks that ambiguity, and also biases the result toward having all-positive 
x,y,z values.


In case it is interesting, my script is here:

http://bl831.als.lbl.gov/~jamesh/scripts/origins.com


You need to have the CCP4 suite set up for it to work.  Run it with no 
arguments to get instructions.


-James Holton

MAD Scientist


On 12/13/2017 5:50 AM, Kajander, Tommi A wrote:

Hello,

If someone could point this out would be very helpful... Wasnt there a simple 
script somewhere that would transfer coordinates close to origin - if they for 
some reason are not? Just cant find anything right away. Sure i have done this 
before...


Thanks,

Tommi

[ccp4bb] EMBO Practical Course on Characterization of macromolecular complexes by integrative structural biology

[Marco Marcia]

Dear ccp4 community,
I would like to remind you of the announcement below.
You can now find the complete programme of the Course following the 
indicated link.

Kind regards,
Marco Marcia

**
EMBO Practical Course on *Characterization of macromolecular complexes 
by integrative structural biology*

May 12-19, 2018
EPN campus
Grenoble, France
http://meetings.embo.org/event/18-characterization

This course has been held biennially since 2002, and covers various 
topics that include methods for expressing and purifying complexes, 
characterizing them biophysically, and probing their structures. It is 
addressed to PhD students and postdocs interested in the structural 
biology of large multisubunit complexes.


*Deadline for registration: 28 February 2018*

We are looking forward to receiving your applications!
Marco
on behalf of the organizing committee: Marco Marcia, Montserrat Soler 
Lopez, Carlo Petosa, Estelle Mossou, Daniele De Sanctis


*

--
_

Dr. Marco MARCIA
Group Leader
EMBL Grenoble
71 Avenue des Martyrs, room 254
38042 Grenoble Cedex 09
France
phone (lab): 0033-(0)47620-7634/7040
phone (office): 0033-(0)47620-7759
fax: 0033-(0)47620-7199
email:mmar...@embl.fr
web:https://embl.fr/research/unit/marcia/  



--
_

Dr. Marco MARCIA
Group Leader
EMBL Grenoble
71 Avenue des Martyrs, room 254
38042 Grenoble Cedex 09
France
phone (lab): 0033-(0)47620-7634/7040
phone (office): 0033-(0)47620-7759
fax: 0033-(0)47620-7199
email: mmar...@embl.fr
web: https://embl.fr/research/unit/marcia/

Re: [ccp4bb] coordinate transformation

[Eleanor Dodson]

I showed you pdbset ..
Find the centre of mass for your assembly.
Move it where you will

pdbset xyzin mow.pdb
end
Find  CoM 0.7 1.3 -0.2

Hmm - a little thought - centre at 1 -1 0   say

pdbset yzin now.pdb xyzout changed.pdb

symgen x , y-2, z

end

New CoM  0.7 -0.7  -0.2

Eleanor





On 18 December 2017 at 00:19, Edward A. Berry  wrote:

> Neat idea!
> And do you have a 1-line command for setting all the coordinates to 1,1,1?
> or 0.1,0.1,0.1 if I still want it near the origin but biased toward the
> inside of the positive-going cell?
> eab
>
>
> On 12/14/2017 07:23 PM, James Holton wrote:
>
>> What I usually do for this is make a copy of the PDB file and change all
>> the atom x-y-z positions to "1.000".  Then I use something like reforigin
>> or my "origins.com" script to shift the original coordinates via allowed
>> symmetry operations, origin shifts, or perhaps indexing ambiguities until
>> it is as close as possible to the "reference", which is at 1,1,1.  I use
>> 1,1,1 instead of 0,0,0 because there are generally at least two
>> symmetry-equivalent places that are equidistant from the origin. Declaring
>> the reference to be a bit off-center breaks that ambiguity, and also biases
>> the result toward having all-positive x,y,z values.
>>
>>
>> In case it is interesting, my script is here:
>>
>> http://bl831.als.lbl.gov/~jamesh/scripts/origins.com
>>
>>
>> You need to have the CCP4 suite set up for it to work.  Run it with no
>> arguments to get instructions.
>>
>>
>> -James Holton
>>
>> MAD Scientist
>>
>>
>> On 12/13/2017 5:50 AM, Kajander, Tommi A wrote:
>>
>>>
>>> Hello,
>>>
>>> If someone could point this out would be very helpful... Wasnt there a
>>> simple script somewhere that would transfer coordinates close to origin -
>>> if they for some reason are not? Just cant find anything right away. Sure i
>>> have done this before...
>>>
>>>
>>> Thanks,
>>>
>>> Tommi
>>>
>>>
>>>
>>

[ccp4bb] PostDoc positions in Membrane Protein Structural Biology

[David Drew]

Dear all,

We are looking for two highly motivated Post-Docs with a Ph.D. in Structural 
biology, Biophysics or related disciplines to work in the lab of David Drew at 
Stockholm University in Sweden. Our international team aims to dissect the 
molecular mechanisms of small molecule transport across membranes (see 
publication: 
http://www.annualreviews.org/doi/abs/10.1146/annurev-biochem-060815-014520). We 
look to employ NMR, cryo EM, X-ray crystallography and other biochemical and 
biophysical approaches to establish how medically-relevant ion and sugar 
transport proteins, central to cell homeostasis, function at the atomic level. 

The Department of Biochemistry and Biophysics has a strong background in 
membrane biology and we have an excellent cryo EM facility with both Titan 
Krios and screening microscopes. You should have a Ph.D. in Structural Biology 
or a related discipline with a strong publication record and a desire to work 
on challenging and multidisciplinary projects. Experience in protein 
expression, purification and cryo EM and/or X-ray crystallography is essential 
for the position. Positions are initially available for 2-years with a 
possibility of extension. 

To apply, please send an email to dd...@dbb.su.se with a single pdf that 
includes your CV and publication record (max 2-pages).

Kind regards,

David Drew

Wallenberg Academy Fellow
Department of Biochemistry and Biophysics
Stockholm University
Sweden

Ph: +46-8-162295
http://www.su.se/profiles/drew-1.181696 

[ccp4bb] EMBL-GSK Postdoctoral Position in Cryo-EM of Chromatin Complexes

[Christoph Mueller]

Dear colleagues,

The Müller group at EMBL Heidelberg in collaboration with 
GlaxoSmithKline (GSK) seeks to recruit an outstanding postdoctoral 
fellow to explore the use of cryo-EM to study small-molecule 
ligand-bound structures of chromatin complexes. The successful candidate 
will apply recent cryo-EM methodological developments to study 
epigenetic targets; develop protocols that increase throughput and 
support lead optimization in drug discovery projects; acquire high 
resolution data sets of ligand-bound chromatin complexes and other 
epigenetic targets.


The successful candidate holds a Ph.D. in structural biology or 
biochemistry. The project is particularly suitable for a postdoctoral 
fellow with solid previous experience in cryo-EM who is interested in 
utilizing and further developing cryo-EM methodology for studying 
epigenetic targets and visualizing small molecule ligands in the drug 
discovery process. The position requires exceptional motivation and 
commitment, the ability to work independently as well as in a team and 
excellent technical, organizational and management skills. A contract of 
2 years, with an optional 3rd year, will be offered to the successful 
candidate.


Closing date for applications is 20 January 2018. Please apply online 
through www.embl.org/jobs 



Best wishes,
Christoph Müller

--

Dr. Christoph W. Müller
Head of Structural and Computational Biology Unit

EMBL
Meyerhofstrasse 1
69117 Heidelberg, Germany

email: cmuel...@embl.de
phone: 0049-6221-387-8320
fax: 0049-6221-387-519
http://www.embl.de
http://www.embl.de/research/units/scb/mueller_christoph/index.html
-

[ccp4bb] Crystallography methods development post at Diamond Light Source

[Graeme Winter]

Good morning all,

We are looking for an enthusiastic methods developer to join the team here at 
Diamond developing integration methods for small molecule X-ray diffraction 
data:

http://www.diamond.ac.uk/Careers/Vacancies/All/132_17_CH.html

The focus of this work is the analysis of more challenging samples brought to 
our dedicated small molecule X-ray diffraction beamline I19. You will work 
closely with the DIALS team, and the post offers an opportunity to work on 
methods development at the boundary between academic research and a major 
scientific facility, where modern open source software development techniques 
are used.

For informal enquiries about this post please feel free to contact me on this 
email address.

For people interested in moving into data analysis but outside of X-ray 
crystallography, I also draw your attention to other data analysis and 
acquisition posts:

http://www.diamond.ac.uk/Careers/Vacancies.html

In particular:

http://www.diamond.ac.uk/Careers/Vacancies/All/136_17_CH.html
http://www.diamond.ac.uk/Careers/Vacancies/All/130_17_CH.html
http://www.diamond.ac.uk/Careers/Vacancies/All/129_17_CH.html
http://www.diamond.ac.uk/Careers/Vacancies/All/128_17_CH.html
http://www.diamond.ac.uk/Careers/Vacancies/All/048_17_CH.html

In all cases the application process is via 
http://www.diamond.ac.uk/Careers/Applicant-Information.html

Best wishes Graeme



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