from:"Sheriff, Steven"

[ccp4bb] Two positions for Associate Research Scientists, Protein Crystallization at Bristol-Myers Squibb Princeton, NJ, USA

2018-09-28 Thread Sheriff, Steven

Bristol-Myers Squibb has two open positions for Associate Research Scientists, 
Protein Crystallization

The only way to apply for these positions are at the following URLs:

https://www.linkedin.com/jobs/view/868141001/
https://www.linkedin.com/jobs/view/868855975/

[If you have questions, please contact 
shannon.ke...@bms.com, Talent Acquisition 
Specialist, R]

Job description

Bristol-Myers Squibb is a global biopharmaceutical company whose mission is to 
discover, develop and deliver innovative medicines that help patients prevail 
over serious diseases.

One shared journey is moving us forward at Bristol-Myers Squibb. Around the 
world, we are passionate about making an impact on the lives of patients with 
serious disease. Empowered to apply our individual talents and ideas so that we 
can learn and grow together. Driven to make a difference, from innovative 
research to hands-on community support. Bristol-Myers Squibb recognizes the 
importance of balance and flexibility in our work environment. We offer a wide 
variety of competitive benefits, services and programs that provide our 
employees the resources to pursue their goals, both at work and in their 
personal lives.

Responsibilities Required

As a key member of the Molecular Structure & Design group, the successful 
candidate will be responsible for crystallization, purification and 
characterization of recombinant proteins utilizing knowledge of conventional 
and affinity chromatography methods, gel electrophoresis, crystallization, and 
general laboratory procedures. As a member of a team involved in the early 
stages of discovery, the position requires close collaboration with molecular 
biologists, protein scientists and structural biologists as well as scientists 
working in the various disease biology and translational areas within 
preclinical research. The candidate must be self motivated, possess excellent 
communication skills, and work both independently as well as in teams. Personal 
attributes of integrity and scientific creativity are required.

Major Skills Required
* BS/MS in Biochemistry, Structural Biology or related field plus 2-6 years of 
experience of industry or academia
* Carry out protein crystallization experiments, crystallization optimization, 
crystal harvesting for proteins and protein ligand complexes.
* Utilize crystallization automation equipment (liquid handlers, drop setters, 
imagers, etc.)
* Carry out protein purification / characterization as well as a thorough 
understanding of protein chromatography principles.
* Capable of independently designing experiments, generating data and 
interpreting results; demonstrated ability to work in a team environment.
* Possesses strong communication skills - be a good listener, have strong, 
concise, and consistent written and oral communication skills.
* The following skills, while not required, would be a plus
*Ability to independently troubleshoot purification systems and protocols.
*Experience in E. coli fermentation and protein expression.
*Experience in X-ray data collection and knowledge of X-ray structure analysis 
is a plus.

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or entity other than the intended recipient is prohibited.



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[ccp4bb] Senior Research Investigator at Bristol-Myers Squibb in X-ray crystallography and cryo-EM

2018-08-16 Thread Sheriff, Steven

All:

Bristol-Myers Squibb has an open Ph.D. level position in X-ray crystallography
and cryo-EM. The only way to apply for this position is through the following
web site:

*
https://bristolmyerssquibb.wd5.myworkdayjobs.com/BMS/job/Princeton---NJ---US/Senior-Research-Investigator_R1508425-1

[Questions or issues with the web site, please contact
michael.kush...@bms.com, Talent Acquisition
Specialist, R]

Bristol-Myers Squibb is a global biopharmaceutical company whose mission is to
discover, develop and deliver innovative medicines that help patients prevail
over serious diseases.

One shared journey is moving us forward at Bristol-Myers Squibb. Around the
world, we are passionate about making an impact on the lives of patients with
serious disease. Empowered to apply our individual talents and ideas so that we
can learn and grow together. Driven to make a difference, from innovative
research to hands-on community support. Bristol-Myers Squibb recognizes the
importance of balance and flexibility in our work environment. We offer a wide
variety of competitive benefits, services and programs that provide our
employees the resources to pursue their goals, both at work and in their
personal lives.

As a key member of the Molecular Structure & Design group, the successful
candidate will be required to have knowledge of and experience in all
structural biology techniques including construct design, expression,
purification, characterization, crystallization, structure determination and
analysis. Strong skills in both X-ray crystallography and single particle
cryoEM is required. The new group member will be involved in early stages of
drug discovery programs which requires close collaboration with molecular
biologists, protein scientists and structural biologists as well as biologists
and chemists working in the various disease biology and translational areas
within preclinical research. The candidate must be self-motivated, possess
excellent communication skills, and work both independently as well as in
teams. Personal attributes of integrity and scientific creativity are required.

Major Skills and Experience Preferred:
oRecombinant protein construct design
oProtein expression and purification
oX-Ray crystallography
oSingle particle cryoEM
oStructure analysis
Experience:
o4-6 years post Ph.D. experience
oPh.D. qualification

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the use of the individual or entity designated above. If you are not the
intended recipient of this message, please notify the sender immediately, and
delete the message and any attachments. Any disclosure, reproduction,
distribution or other use of this message or any attachments by an individual
or entity other than the intended recipient is prohibited.

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[ccp4bb] Bristol-Myers Squibb Princeton has an open position for BS/MS level scientist

2017-03-22 Thread Sheriff, Steven

The only way to apply for this position is through the URL:

https://bms.taleo.net/careersection/jobdetail.ftl?job=1701159=en#.WNF-OPIUNfo.mailto
However, here is the job description ...

Job Description
Associate Research Scientist (Job Number:  1701159)
Description

Bristol-Myers Squibb is a global biopharmaceutical company whose mission is to 
discover, develop and deliver innovative medicines that help patients prevail 
over serious diseases.
One shared journey is moving us forward at Bristol-Myers Squibb. Around the 
world, we are passionate about making an impact on the lives of patients with 
serious disease. Empowered to apply our individual talents and ideas so that we 
can learn and grow together. And driven to make a difference, from innovative 
research to hands-on community support. Bristol-Myers Squibb recognizes the 
importance of balance and flexibility in our work environment. We offer a wide 
variety of competitive benefits, services and programs that provide our 
employees the resources to pursue their goals, both at work and in their 
personal lives.
Bristol-Myers Squibb recognizes the importance of balance and flexibility in 
our work environment. We offer a wide variety of competitive benefits, services 
and programs that provide our employees the resources to pursue their goals, 
both at work and in their personal lives.
As a key member of the Molecular Structure & Design group, the successful 
candidate will be responsible for crystallization, purification and biophysical 
characterization of recombinant proteins using knowledge of conventional and 
affinity chromatography methods, gel electrophoresis, crystallization, and 
general laboratory procedures.  As a member of a team involved in the early 
stages of discovery, the position requires close collaboration with molecular 
biologists, protein scientists and structural biologists as well as scientists 
working in the various disease biology and translational areas within 
preclinical research. The candidate must be self-motivated, possess excellent 
communication skills, and work both independently as well as in teams. Personal 
attributes of integrity and scientific creativity are required.

Qualifications

-  BS/MS in Biochemistry, Structural Biology or related field required
-  2-5 years experience required
-  Carry out protein crystallization experiments, crystallization optimization, 
crystal harvesting for proteins, protein-ligand complexes, and protein-protein 
complexes and X-ray data collection.
-  Use crystallization automation equipment (liquid handlers, drop setters, 
imagers, etc.)
-  Carry out protein purification / biophysical characterization as well as 
thoroughly understands protein chromatography principles.
-  Capable of independently designing experiments, generating data and 
interpreting results; demonstrated ability to work in a team environment.
-  Possesses strong communication skills - be a good listener, have strong, 
concise, and consistent written and oral communication skills.

Bristol-Myers Squibb is an equal opportunity employer - Vet/Disability



This message (including any attachments) may contain confidential, proprietary, 
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[ccp4bb] FW: New ligand 3-letter code (help-7071)

2015-06-19 Thread Sheriff, Steven

All:

Since the original query was cross-posted on both the COOT mailing list and the 
CCP4BB Rachel Green gave me permission to forward this to both. She provides 
links about the mechanism of assignment of 3-letter codes. In the third link 
below, my original suggestion to the COOT mailing list that one could just use 
UNK is incorrect as that is reserved for unknown amino acids. According to this 
document, I should have suggested UNL for an unknown ligand.

Steven

From: Rachel Kramer Green [mailto:kra...@rcsb.rutgers.edu]
Sent: Tuesday, June 16, 2015 10:21 AM
To: Sheriff, Steven
Cc: info
Subject: Re: New ligand 3-letter code (help-7071)

Dear Steven,

During annotation of ligands, all chemical components present in the structure 
are compared against the definitions in the Chemical Component Dictionary 
(http://www.wwpdb.org/data/ccd). If the ligand is not in the dictionary, a 
three letter code is assigned. See 
http://www.wwpdb.org/documentation/policy#toc_assignment.  In the future, a 
group of three-letter codes may be set aside to be used during refinement to 
flag new ligands.

Clarification about the ligand ids assignment and in particular the usage of 
UNX/UNL/UNK residues can be found at 
http://www.wwpdb.org/documentation/procedure#toc_2.

Best wishes,
Rachel


Rachel Kramer Green, Ph.D.
RCSB PDB
kra...@rcsb.rutgers.edumailto:kra...@rcsb.rutgers.edu

New! Deposit X-ray data with the wwPDB at:
http://deposit.wwpdb.org/deposition (NMR and 3DEM coming soon).
___
Twitter: https://twitter.com/#!/buildmodels
Facebook: http://www.facebook.com/RCSBPDB



On 6/5/2015 7:50 AM, Sheriff, Steven wrote:
All:

Why the concern for unassigned three-letter codes? The wwPDB isn’t going to let 
you assign a three-letter code, it will choose its own code.

At BMS (a pharmaceutical company), we do many hundreds of structures a year 
with ligands and we assign the same, already assigned, three-letter code for 
all of our ligands (unless we have two or more different ligands in a single 
structure, in which case we use two or more different already assigned 
three-letter codes).  COOT can mostly handle this.

However, I believe that if you want an unassigned code, the wwPDB has set aside 
UNK[nown] for this purpose.

Steven

From: Mailing list for users of COOT Crystallographic Software 
[mailto:c...@jiscmail.ac.uk] On Behalf Of Eleanor Dodson
Sent: Friday, June 05, 2015 6:28 AM
To: c...@jiscmail.ac.ukmailto:c...@jiscmail.ac.uk
Subject: Re: New ligand 3-letter code

I use your method - trial  error..
It would be nice if at least there was a list somewhere of unassigned codes!

On 5 June 2015 at 09:16, Lau Sze Yi (SIgN) 
lau_sze...@immunol.a-star.edu.sgmailto:lau_sze...@immunol.a-star.edu.sg 
wrote:
Hi,

What is the proper way of generating 3-letter code for a new ligand? As of now, 
I insert my ligand in Coot using smiles string and for the 3-letter code I 
picked a non-existent code by trial and error (not very efficient). A cif file 
with corresponding name which I generated using Phenix was imported into Coot.

I am sure there is a proper way of doing this. Appreciate your feedback.

Regards,
Sze Yi


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This message (including any attachments) may contain confidential, proprietary, 
privileged and/or private information. The information is intended to be for 
the use of the individual or entity designated above. If you are not the 
intended recipient of this message, please notify the sender immediately, and 
delete the message and any attachments. Any disclosure, reproduction, 
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or entity other than the intended recipient is prohibited.

Re: [ccp4bb] on NCS restraint

2015-04-21 Thread Sheriff, Steven

All:



I strongly disagree with Reza's suggestion that one should abandon NCS at 
better than 2.5 Å resolution (or even Herman's suggestion at better than 2.0 Å 
resolution). Either of these may be true in any particular case, BUT one should 
do the experiment - Run parallel refinements from the same starting model with 
and without NCS restraints and compare R-free, the gap between R-free and 
R-work, and particular places where one knows or suspects that the local 
geometry is different, before deciding to abandon NCS restraints. This was 
certainly true in the bad old days when loose (as opposed to strict) NCS 
restraints were used and bound each chain more-or-less to a single chain's 
geometry, even though one was refining all extant chains. Using so-called 
loose NCS restraints, I once had a loop pulled out of electron density during 
refinement and the tip moved ~6 Å!



However, for the last 5 years or so, BUSTER, which I use, and REFMAC (and 
presumably PHENIX) have used LSSR (local secondary structure restraints) where 
the maximum pull to uniformity tops out at a certain value. I have not 
rigorously followed my own advice above to run parallel refinements, but I have 
yet to find a case where LSSR-type NCS restraints have hurt the refinement 
down to at least ~1.5 Å resolution.



To give credit where it is due, Oliver Smart, who implemented LSSR in BUSTER, 
attributed the concept to George Sheldrick.



Steven



--

Date:Mon, 20 Apr 2015 10:38:27 +

From:Reza Khayat rkha...@ccny.cuny.edumailto:rkha...@ccny.cuny.edu

Subject: Re: [ccp4bb] on NCS restraint



Hi,



The purpose of NCS is to reduce the degrees of freedom in order to avoid over 
refinement -not only to expedite refinement. Strict or restrained NCS should be 
applied at lower resolutions (2.7Å) or data completeness. Forgo NCS If you 
have a complete and better than 2.5Å dataset. Also, you can define the regions 
where NCS is applied and thus avoid loops/regions where the NCS is violated.



Best wishes,

Reza



Reza Khayat, PhD

Assistant Professor

City College of New York

160 Convent Ave, MR-1135

New York, NY 10031

(212) 650-6070

rkha...@ccny.cuny.edumailto:rkha...@ccny.cuny.edumailto:rkha...@ccny.cuny.edu%3cmailto:rkha...@ccny.cuny.edu



--

On Apr 20, 2015, at 4:01 AM, 
herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com%3cmailto:herman.schreu...@sanofi.com
 wrote:



Dear Smith,



There used to be something called strict NCS which meant that instead of many 
identical subunits, only one average subunit was refined, which would speed 
up the refinement significantly, at the expense of requiring that all subunits 
are exactly identical.



I do not think that this option is used anymore and most refinement programs 
would require NCS related subunits to be similar, but not identical to each 
other. As Robbie Joosten pointed at, this can help a lot, especially when you 
do not have high resolution data. So for data with better than 2.0 Å 
resolution, including NCS restraints would probably not make a big difference, 
but otherwise I would switch them on.



Best,

Herman



--

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Smith Liu

Gesendet: Freitag, 17. April 2015 06:02

An: 
CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK%3cmailto:CCP4BB@JISCMAIL.AC.UK

Betreff: Re: [ccp4bb] on NCS restraint



Dear Jurgen,



My understanding is that NCS restraint can significantly enhance the speed of 
calculation, but considering the subunits even with the eactly same sequence 
may not be identical, to have NCS restraint may be not necessary or may be not 
good for the refinement, am I right?



Smith



At 2015-04-17 09:09:05, Jurgen Bosch 
jbos...@jhu.edumailto:jbos...@jhu.edumailto:jbos...@jhu.edu%3cmailto:jbos...@jhu.edu
 wrote:



yes.

Have two sets of NCS operators one that describe the four subunits and one 
describing the two subunits. If during the refinement of your structure you 
should find out that the subunits are not identical to each other you can relax 
the NCS weights.



Jürgen

..

Jürgen Bosch

Johns Hopkins University

Bloomberg School of Public Health

Department of Biochemistry  Molecular Biology Johns Hopkins Malaria Research 
Institute

615 North Wolfe Street, W8708

Baltimore, MD 21205

Office: +1-410-614-4742tel:%2B1-410-614-4742

Lab:  +1-410-614-4894tel:%2B1-410-614-4894

Fax:  +1-410-955-2926tel:%2B1-410-955-2926

http://lupo.jhsph.eduhttp://lupo.jhsph.edu/http://lupo.jhsph.edu%3chttp:/lupo.jhsph.edu/



--

On Apr 16, 2015, at 9:02 PM, Smith Lee 
0459ef8548d5-dmarc-requ...@jiscmail.ac.ukmailto:0459ef8548d5-dmarc-requ...@jiscmail.ac.ukmailto:0459ef8548d5-dmarc-requ...@jiscmail.ac.uk%3cmailto:0459ef8548d5-dmarc-requ...@jiscmail.ac.uk

Re: [ccp4bb] on NCS restraint

2015-04-21 Thread Sheriff, Steven

All:

Oops, someone pointed out to me off line that I slipped-up earlier today when I 
wrote that  LSSR is an abbreviation for Local Secondary Structure 
Restraints. Rather it is an abbreviation for  Local Structure Similarity 
Restraints. I know better, but I guess my unconscious got the better of me.

Steven

From: Victor Lamzin [mailto:vic...@embl-hamburg.de]
Sent: Tuesday, April 21, 2015 9:07 AM
To: Sheriff, Steven; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] on NCS restraint


Hi all,

We have carried out a large-scale test of the use of Refmac's NCS-restraints 
during model building with ARP/wARP. We have found advantageous to have such 
restraints turned on with data resolution extending to as high as 1.5 A.

Victor



On 21/04/2015 14:46, Sheriff, Steven wrote:

All:



I strongly disagree with Reza's suggestion that one should abandon NCS at 
better than 2.5 Å resolution (or even Herman's suggestion at better than 2.0 Å 
resolution). Either of these may be true in any particular case, BUT one should 
do the experiment - Run parallel refinements from the same starting model with 
and without NCS restraints and compare R-free, the gap between R-free and 
R-work, and particular places where one knows or suspects that the local 
geometry is different, before deciding to abandon NCS restraints. This was 
certainly true in the bad old days when loose (as opposed to strict) NCS 
restraints were used and bound each chain more-or-less to a single chain's 
geometry, even though one was refining all extant chains. Using so-called 
loose NCS restraints, I once had a loop pulled out of electron density during 
refinement and the tip moved ~6 Å!



However, for the last 5 years or so, BUSTER, which I use, and REFMAC (and 
presumably PHENIX) have used LSSR (local secondary structure restraints) where 
the maximum pull to uniformity tops out at a certain value. I have not 
rigorously followed my own advice above to run parallel refinements, but I have 
yet to find a case where LSSR-type NCS restraints have hurt the refinement 
down to at least ~1.5 Å resolution.



To give credit where it is due, Oliver Smart, who implemented LSSR in BUSTER, 
attributed the concept to George Sheldrick.



Steven



--

Date:Mon, 20 Apr 2015 10:38:27 +

From:Reza Khayat rkha...@ccny.cuny.edumailto:rkha...@ccny.cuny.edu

Subject: Re: [ccp4bb] on NCS restraint



Hi,



The purpose of NCS is to reduce the degrees of freedom in order to avoid over 
refinement -not only to expedite refinement. Strict or restrained NCS should be 
applied at lower resolutions (2.7Å) or data completeness. Forgo NCS If you 
have a complete and better than 2.5Å dataset. Also, you can define the regions 
where NCS is applied and thus avoid loops/regions where the NCS is violated.



Best wishes,

Reza



Reza Khayat, PhD

Assistant Professor

City College of New York

160 Convent Ave, MR-1135

New York, NY 10031

(212) 650-6070

rkha...@ccny.cuny.edumailto:rkha...@ccny.cuny.edumailto:rkha...@ccny.cuny.edu%3cmailto:rkha...@ccny.cuny.edu



--

On Apr 20, 2015, at 4:01 AM, 
herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com%3cmailto:herman.schreu...@sanofi.com
 wrote:



Dear Smith,



There used to be something called strict NCS which meant that instead of many 
identical subunits, only one average subunit was refined, which would speed 
up the refinement significantly, at the expense of requiring that all subunits 
are exactly identical.



I do not think that this option is used anymore and most refinement programs 
would require NCS related subunits to be similar, but not identical to each 
other. As Robbie Joosten pointed at, this can help a lot, especially when you 
do not have high resolution data. So for data with better than 2.0 Å 
resolution, including NCS restraints would probably not make a big difference, 
but otherwise I would switch them on.



Best,

Herman



--

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Smith Liu

Gesendet: Freitag, 17. April 2015 06:02

An: 
CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK%3cmailto:CCP4BB@JISCMAIL.AC.UK

Betreff: Re: [ccp4bb] on NCS restraint



Dear Jurgen,



My understanding is that NCS restraint can significantly enhance the speed of 
calculation, but considering the subunits even with the eactly same sequence 
may not be identical, to have NCS restraint may be not necessary or may be not 
good for the refinement, am I right?



Smith



At 2015-04-17 09:09:05, Jurgen Bosch 
jbos...@jhu.edumailto:jbos...@jhu.edumailto:jbos...@jhu.edu%3cmailto:jbos...@jhu.edu
 wrote:



yes.

Have two sets of NCS operators one that describe the four subunits and one 
describing the two subunits. If during the refinement of your structure you 
should find out that the subunits are not identical to each other you can relax

Re: [ccp4bb] Molecular Replacement model preparation

2014-10-07 Thread Sheriff, Steven

All:



While Phil Jeffrey attributed to me the trick of aligning the hinge axis of 
an Fab along the Z direction, I, in turn, must give credit to Mirek Cygler, who 
explained this to me at the Diffraction Methods in Molecular Biology [now 
Structural Biology] Gordon Research Conference in 1986.



To Scott's query about searching for 1 domain sequentially and then other 
domains OR searching for multiple domains all at once?



Inevitably a program like PHASER searches for domains (ensembles in its 
terminology) sequentially. However, as to the practical question of whether to 
feed PHASER all of the domains in one run, that is certainly how I start and 
it is usually (almost always?) successful. In fact, while I no longer bother to 
align the hinge axis of an Fab along the Z axis, I now break Fabs into three 
parts: CL:CH1, VH, and VL to allow molecular replacement to accommodate the 
tilt angle between VH and VL (tilt angle is a term I learned from Gary 
Gilliland's talk at the Diffraction Methods in Structural Biology GRC in 2014). 
This also allows me to search for the highest identity VL and, separately, VH 
in the PDB to use as probe models.  N.B. since I'm usually studying antigen/Fab 
complex, I'm usually searching for 4 ensembles in one PHASER run: CL:CH1, 
antigen, VH and VL.



Steven



P.S. to Tassos Perrakis: I'm sorry that these plugs for the Diffraction Methods 
GRC are ~4 months too late!

P.P.S. to Eddie Snell: And I'm sorry that these plugs are ~18 months too early 
for 2016's Diffraction Methods GRC!





==

Date:Mon, 6 Oct 2014 18:33:26 +

From:Scott Thomas Walsh swals...@umd.edumailto:swals...@umd.edu

Subject: Re: Molecular Replacement model preparation



Hi Phil,



Thank you for the input.  I would like to get CCP4ers input.  I deal with 
multiple domain cytokine receptors in a manner very similar to antibody 
molecules.



Have people have more correct solutions searching for 1 domain sequentially and 
then other domains OR searching for multiple domains all at once?  I am curious 
to hear peoples' experiences on this topic?



Cheers,



Scott





Scott T. R. Walsh, PhD

Assistant Professor

University of Maryland

IBBR/CBMG

3127E CARB-2

9600 Gudelsky Drive

Rockville, MD  20850  USA

phone: (240) 314-6478

fax: (240) 314-6225

email: swals...@umd.edumailto:swals...@umd.edu





On Oct 6, 2014, at 2:11 PM, Phil Jeffrey 
pjeff...@princeton.edumailto:pjeff...@princeton.edu wrote:



 That document is fairly old and is in dire need of revision to reflect the 
 modern arsenal of programs.



 Nevertheless:

 Putting the hinge axis along Z was a trick told to me by Steven Sheriff back 
 in the days when we worked on Fab structures - which after all are classical 
 examples of hinged molecules.  One would search with separate domain 
 fragments - split either side of the hinge - and the Z-orientation trick 
 makes it easier to spot pairs of peaks from each search model that are 
 related to each other.  In the Fab world we searched with Fv models (VH:VL 
 heterodimer) and CH1:CL constant region heterodimeric models.  Peaks related 
 solely by hinge motion would have similar alpha and beta angles and 
 potentially different gamma (Crowther convention Eulerian angles).  
 Historical note: this was back in the days when it was possible to remember 
 the names of all the Fab fragments that were in PDB and their respective IDs.



 This ploy was more important in the days before Phaser or Molrep, which will 
 now gleefully try a long list of rotation function peaks for you quite 
 quickly, so manually parsing the list of rotation function peaks is rather 
 unnecessary.  And perhaps counter-productive.





 Split your molecule apart at the hinge, giving fragment1 and fragment2.  
 Attempt to find both fragments independently.  Choose the one that gives the 
 best results: TFZ score or LLG score or discrimination between possible space 
 group or whatever you like.  Then, attempt to find the *other* fragment in 
 the context of that first solution.





 Phil Jeffrey

 Princeton





 On 10/5/14 3:34 AM, Luzuokun wrote:

 Dear all,

 I'm doing molecular replacement using Phaser. My protein is predicted

 to have two domain with a hinge linking them. The model sequence

 identity is 0.27. But the MR result is poor. I've tried other

 programme (Molrep, MrBump, Balbes,,,_.) But no improvement was

 observed. I think that this is due to the open or closed

 conformation around the hinge. I was told that I could place the Z

 axis along the hinge

 (http://xray0.princeton.edu/~phil/Facility/Guides/MolecularReplacemen

 t.html),  could anyone tell me more details about how to do next?



 Thanks!

 Lu Zuokun





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[ccp4bb] ASSOCIATE RESEARCH SCIENTIST II - PROTEIN CRYSTALLIZATION

2014-08-05 Thread Sheriff, Steven

I enclose a description of a new open position at Bristol-Myers Squibb (BMS) in
Princeton, New Jersey, USA. The only way to apply for the position is through
the BMS web site: Associate Research Scientist II - Protein
Crystallizationhttps://bms.taleo.net/careersection/jobdetail.ftl?job=1403777lang=ensns_id=mailto#.U9btF7F0Et4.mailto.
Therefore, please do NOT email me directly. Specifically, I am NOT the hiring
manager.

ASSOCIATE RESEARCH SCIENTIST II - PROTEIN CRYSTALLIZATION (Job Number: 1403777)

Description

As a key member of the Molecular Structure Design group, the successful
candidate will be responsible for crystallization, purification and
characterization of recombinant proteins utilizing knowledge of conventional
and affinity chromatography methods, gel electrophoresis, crystallization, and
general laboratory procedures. As a member of a team involved in the early
stages of discovery, the position requires close collaboration with molecular
biologists, protein scientists and structural biologists as well as scientists
working in the various disease biology and translational areas within
preclinical research. The candidate must be self motivated, possess excellent
communication skills, and work both independently as well as in teams. Personal
attributes of integrity and scientific creativity are required.

Qualifications

* BS/MS in Biochemistry, Structural Biology or related field plus 2-5 years of
experience of industry or academia
* Carry out protein crystallization experiments, crystallization optimization,
crystal harvesting for proteins and protein ligand complexes.
* Utilize crystallization automation equipment (liquid handlers, drop setters,
imagers, etc.)
* Carry out protein purification / characterization as well as a thorough
understanding of protein chromatography principles.
* Experience in X-ray data collection and knowledge of X-ray structure analysis
is a plus.
* Capable of independently designing experiments, generating data and
interpreting results; demonstrated ability to work in a team environment.
* Possesses strong communication skills - be a good listener, have strong,
concise, and consistent written and oral communication skills.

Bristol-Myers Squibb is an equal opportunity employer - M/F/Vet/Disability

[ccp4bb] Test [My apologies]

2012-10-05 Thread Sheriff, Steven

My apologies to all for this apparent spam, but one of my colleagues signed up 
for the CCP4BB recently and despite Ronan Keegan checking that his account has 
been activated, he has not been receiving CCP4B email.  I'm trying to help him 
track down the problem with this email.


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or entity other than the intended recipient is prohibited.

Re: [ccp4bb] dumb software question

2012-08-08 Thread Sheriff, Steven

All:

Joel's attempt to post an interesting article somehow got concatenated 3 times. 
 The URL should be:

http://www.rdmag.com/News/2012/08/Life-Science-Biology-Microscopy-Virtual-nanoscop-Like-Google-Earth-for-cell-biologists/?et_cid=2784615et_rid=54732139

Also in an off-board conversation, Joel pointed out some work done by his group 
that looks interesting and useful:

proteopedia.orghttp://proteopedia.org

Steven


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or entity other than the intended recipient is prohibited.

Re: [ccp4bb] Announcing a Web Server for the Grade ligand restraints generator.

2012-03-21 Thread Sheriff, Steven

All:

I would like to second Herman Schreuder's witty repartee (and Steve Soisson's 
and Ian Tickle's comments referred to in a post by Oliver Smart) that using 
GRADE will be an upgrade to the standard CIF dictionaries.

Steven


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Re: [ccp4bb] van der Waals distances

2012-03-21 Thread Sheriff, Steven

David:

In my experience most people don't put a lot of thought into an upper limit for 
van der Waals (VDW) contacts and use a hard, arbitrary upper value of 4 
Angstrom.

In the mid-1980's, Wayne Hendrickson and I proposed that one should use:

· Atom type dependent cutoffs

· As an approximation to the asymptote to zero energy at infinite 
distance, an upper bound that was as much above the distance of minimum energy 
(Rmin) as Rmin was above the zero energy, Rzero, which is the point at which 
the repulsive forces exceed the attractive forces. Using a form of a 6-12 
potential, we calculated that Rlimit = 1.11 x Rmin (and that Rzero = 0.89 x 
Rmin).

I have used that in all my succeeding work, e.g. on antibodies, although during 
a stint in David Davies' group at NIH following working with Wayne at the Naval 
Research Laboratory, I switched from using the very simple 4 atom types that 
PROTIN used to a somewhat more complex set of values that I was introduced to 
based on a paper by Gelin  Karplus (1979).

Here are some references:

S. Sheriff, W. A. Hendrickson  J. L. Smith (1987).  The Structure of 
Myohemerythrin in the Azidomet State at 1.7/1.3 Å Resolution.  J. Mol. Biol. 
197, 273-296.

S. Sheriff (1993).  Some Methods for Examining the Interaction between Two 
Molecules.  Immunomethods 3, 191-196.

B. R. Gelin  M. Karplus (1979).  Side-Chain Torsional Potentials: Effect of 
Dipeptide, Protein, and Solvent Environment.  Biochemistry 18, 1256-1268.

And here are some reviews that used that used this calculation to compare 
structures:

D. R. Davies, E. A. Padlan  S. Sheriff (1990).  Antibody-Antigen Complexes.  
Annu. Rev. Biochem. 59, 439-473.

S. Sheriff (1993). Antibody - Protein Complexes.  Immunomethods 3, 222-227.

Papers on antibody/antigen complexes that were edited by Ian Wilson in his 
capacity as an editor of J. Mol. Biol. were often requested to use the 
methodology as well.  Unfortunately [ ;) ], too many papers appeared outside of 
J. Mol. Biol. that were ignorant of the methodology put in place by me and used 
by Ian's group at Scripps as evidenced by (although these report on buried 
surface area calculations):

I.  A. Wilson  R. L. Stanfield (1993). Antibody-antigen interactions (1993). 
Curr. Opin. Struct. Biol. 3, 113-118.

I.  A. Wilson  R. L. Stanfield (1994). Antibody-antigen interactions: new 
structures and new conformational changes (1994). Curr. Opin. Struct. Biol. 4, 
857-867.

for these methods to remain the standard in the field.

In the department of totally shameless self-promotion (as opposed to the above 
shameless self-promotion), I have published a recent paper, where I have used 
this methodology for the field of 10Fn3-based variants, when used as binding 
proteins in a manner analogous to antibodies, or more similarly, VHH domains 
(Camelid-like VH domains):

V. Ramamurthy, S. R. Krystek, Jr., A. Bush, A. Wei, S. Emanuel, R. DasGupta, A. 
Janjua, Z. Lin, L. Cheng, M. Murdock, D. Cohen, P. Morin, J. H. Davis, M. 
Dabritz, D. C. McLaughlin, K. A. Russo, G. Chao, M. C. Wright, V. A. Jenny, L. 
J. Engle, E. Furfine  S. Sheriff (2012).  Structures of Adnectin/Protein 
complexes reveal an expanded binding footprint.  Structure, 20, 259-269.

Steven



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Re: [ccp4bb] Open position at Bristol-Myers Squibb (Princeton, NJ, USA) Third time is the charm?

2012-01-04 Thread Sheriff, Steven

CONTACT ME ONLY IF YOU HAVE TECHNICAL DIFFICULTIES WITH THE LINK OR THE ONLINE
APPLICATION PROCESS. DESCRIBE YOUR PROBLEM AND I WILL FORWARD IT TO BMS HUMAN
RESOURCES. SENDING ANYTHING ELSE DIRECTLY TO ME WILL BE PERCEIVED AS AN
INABILITY TO FOLLOW SIMPLE DIRECTIONS AND CAUSE TO CONSIDER DISCARDING YOUR
APPLICATION.

RESEARCH INVESTIGATOR I-1105118

Job Description

* As a key member of the Protein Science and Structures team, the successful
candidate will be responsible for purification, characterization, and
crystallization of recombinant proteins utilizing knowledge of conventional and
affinity chromatography methods, gel electrophoresis, crystallization, and
general laboratory procedures.
* As a member of a team involved in the early stages of discovery, the
position requires close collaboration with molecular biologists and structural
biologists as well as scientists working in the various disease biology and
translational areas within preclinical research.
* The candidate must be self-motivated, possess good communication skills,
and work both independently as well as in teams.
* Personal attributes of integrity and scientific creativity are required.

Qualifications

* The successful candidate is required to have experience in protein
crystallization, harvesting, and data collection.
* The candidate should also be familiar with the methods of determining
protein X-ray structures including indexing/scaling of data, structure
determination through molecular replacement and other techniques, refinement,
and analysis of the resulting structure.
* The candidate is also required to have experience in protein purification
/ characterization as well as a thorough understanding of protein
chromatography principles.
* Demonstrated ability to devise and implement novel multi-step purification
using protein chromatography workstations is sought (e.g. AKTA
Purifier/Explorer, gel filtration, ion exchange chromatography,
microfiltration, and other related techniques) as applied to materials from
microbial and eukaryotic expression sources (secreted inclusion bodies).
* Capable of independently designing experiments, generating data and
interpreting results; demonstrated ability to work in a team environment. Good
listener. Strong, concise, and consistent written and oral communication
required.
* Ability to independently troubleshoot HPLC and other purification systems
and protocols a plus.
* Experience in E coli fermentation / protein expression a plus.
PH.D. in Biochemistry, Structural Biology, or related field. 0-5 years
experience.

Apply
onlinehttps://bms.taleo.net/careersection/ejs+external+career+site+w2fprofile+ques+v20090518/jobdetail.ftl?lang=enjob=37757
to this position.

N.B. You will receive a confirmation email after successfully completing the
online application.

[ccp4bb] Open position at Bristol-Myers Squibb (Princeton, NJ, USA)

2012-01-03 Thread Sheriff, Steven

RESEARCH INVESTIGATOR I-1105118

Job Description

Qualifications

PH.D. in Biochemistry, Structural Biology, or related field. 0-5 years
experience.

Apply
onlinehttps://bms.taleo.net/careersection/ejs+external+career+site+w2fprofile+ques+v20090518/jobdetail.ftl?lang=enjob=37757
to this position.

Re: [ccp4bb] Open position at Bristol-Myers Squibb (Princeton, NJ, USA)

2012-01-03 Thread Sheriff, Steven

All:

I am not the hiring manager, although I, along with the rest of the
crystallography team, will be involved in the hiring process. Please contact
me only if you are unable to use the link in the original email (which is
below). Otherwise please submit your application online.

Steven

RESEARCH INVESTIGATOR I-1105118

Job Description

Qualifications

PH.D. in Biochemistry, Structural Biology, or related field. 0-5 years
experience.

Apply
onlinehttps://bms.taleo.net/careersection/ejs+external+career+site+w2fprofile+ques+v20090518/jobdetail.ftl?lang=enjob=37757
to this position.

[ccp4bb] Diffraction Data Deposition - Data Woes in general

2011-12-02 Thread Sheriff, Steven

All:

The recent discussion on the CCP4BB about Diffraction Data Deposition made me 
think at that at least certain people might be interested in an article in 
Thursday, Dec. 1, New York Times business section entitled A Genome Deluge in 
the print version:

http://www.nytimes.com/2011/12/01/business/dna-sequencing-caught-in-deluge-of-data.html?_r=1scp=1sq=Genome%20Delugest=Search

It makes the woes of crystallography data seem tame by comparison.

Steven


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delete the message and any attachments. Any disclosure, reproduction, 
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or entity other than the intended recipient is prohibited.

[ccp4bb] Program SC

2010-07-16 Thread Sheriff, Steven

All:

We are running CCP4 v6.1.3.  I have recently tried to use the Program SC, which 
calculates Surface Complementarity of an interface between two components.  I 
can get it to run fine, but I have one complex, where one of the partners has 
carbohydrate residues, which have atoms that are not part of the standard 
library, sc_radii.lib.  The sc.doc file notes that one can use one's own atomic 
radii library by adding the keyword, SCRADII to the command line, i.e.

% sc XYZIN foo.pdb SCRADII my_radii.lib

However, the log file shows that SC is continuing to use $CLIBD/sc_radii.lib, 
rather than the library I have tried to provide.


* Has anyone had any recent experience using SC with using their own 
radii library?

o   If so, how did you make it work?

* Is it possible that this program is used so rarely that the mechanism 
for using one's own radii library was accidentally broken and no one noticed?

Steven


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Re: [ccp4bb] Program SC

2010-07-16 Thread Sheriff, Steven

Ian:

Thank you for responding at 22:00 on a Friday evening.

Your suggestion of using ./my_radii.lib led to the program recognizing the file.

CCP4 should considering modifying the sc.doc document to make the fact that the 
directory needs to be specified explicit.

Steven

From: Ian Tickle [mailto:ianj...@gmail.com]
Sent: Friday, July 16, 2010 5:02 PM
To: Sheriff, Steven
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Program SC


Hi Steven

SCRADII is defined in $CINCL/defaults.def which if I recall correctly implies 
that by default it will look in $CLIBD for the file, unless you specify a 
directory explicitly.

So you could try:

% sc XYZIN foo.pdb SCRADII ./my_radii.lib

Hope it works!

Cheers

-- Ian
On Fri, Jul 16, 2010 at 9:10 PM, Sheriff, Steven 
steven.sher...@bms.commailto:steven.sher...@bms.com wrote:
All:

We are running CCP4 v6.1.3.  I have recently tried to use the Program SC, which 
calculates Surface Complementarity of an interface between two components.  I 
can get it to run fine, but I have one complex, where one of the partners has 
carbohydrate residues, which have atoms that are not part of the standard 
library, sc_radii.lib.  The sc.doc file notes that one can use one's own atomic 
radii library by adding the keyword, SCRADII to the command line, i.e.

% sc XYZIN foo.pdb SCRADII my_radii.lib

However, the log file shows that SC is continuing to use $CLIBD/sc_radii.lib, 
rather than the library I have tried to provide.


* Has anyone had any recent experience using SC with using their own 
radii library?

o   If so, how did you make it work?

* Is it possible that this program is used so rarely that the mechanism 
for using one's own radii library was accidentally broken and no one noticed?

Steven


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privileged and/or private information. The information is intended to be for 
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intended recipient of this message, please notify the sender immediately, and 
delete the message and any attachments. Any disclosure, reproduction, 
distribution or other use of this message or any attachments by an individual 
or entity other than the intended recipient is prohibited.



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privileged and/or private information. The information is intended to be for 
the use of the individual or entity designated above. If you are not the 
intended recipient of this message, please notify the sender immediately, and 
delete the message and any attachments. Any disclosure, reproduction, 
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or entity other than the intended recipient is prohibited.

[ccp4bb] Two positions for Associate Research Scientists, Protein Crystallization at Bristol-Myers Squibb Princeton, NJ, USA

[ccp4bb] Senior Research Investigator at Bristol-Myers Squibb in X-ray crystallography and cryo-EM

[ccp4bb] Bristol-Myers Squibb Princeton has an open position for BS/MS level scientist

[ccp4bb] FW: New ligand 3-letter code (help-7071)

Re: [ccp4bb] on NCS restraint

Re: [ccp4bb] on NCS restraint

Re: [ccp4bb] Molecular Replacement model preparation

[ccp4bb] ASSOCIATE RESEARCH SCIENTIST II - PROTEIN CRYSTALLIZATION

[ccp4bb] Test [My apologies]

Re: [ccp4bb] dumb software question

Re: [ccp4bb] Announcing a Web Server for the Grade ligand restraints generator.

Re: [ccp4bb] van der Waals distances

Re: [ccp4bb] Open position at Bristol-Myers Squibb (Princeton, NJ, USA) Third time is the charm?

[ccp4bb] Open position at Bristol-Myers Squibb (Princeton, NJ, USA)

Re: [ccp4bb] Open position at Bristol-Myers Squibb (Princeton, NJ, USA)

[ccp4bb] Diffraction Data Deposition - Data Woes in general

[ccp4bb] Program SC

Re: [ccp4bb] Program SC

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