[ccp4bb] Job opening at the Albany College of Pharmacy and Health Sciences

2017-10-06 Thread Manish Shah 
Dear colleagues,

Please forward the following open position in molecular and structural
biology to potential candidates.

https://employment.acphs.edu/postings/490


Thank you.

Manish




Manish  B.  Shah,  Ph.D.

Assistant Professor

Department of Pharmaceutical Sciences

Albany College of Pharmacy and Health Sciences

Bioscience Research Building, 104C

106 New Scotland Avenue

Albany, NY 12208

Phone: (518) 694-7343

Fax: (518) 694-7499

Email: manish.s...@acphs.edu

Re: [ccp4bb] HKL to mtz

2017-10-06 Thread SLAC 
You know, after f2mtz you can often have an mtz file with an unconventional ASU 
setting or unknown sort order. This breaks certain programs. So, I always run 
the result of f2mtz through a do-nothing run of the program called "CAD". Even 
if you don't tell it to do anything CAD always produces a "saeitized" output 
mtz. Have you tried that?

-James Holton
MAD Scientist

> On Oct 5, 2017, at 8:01 PM, ameya benz  wrote:
> 
> Hi,
> 
> I want to convert HKL file to mtz. I tried using F2mtz but somehow the output 
> mtz is not working. What parameters should I set during conversion. Or can 
> anyone suggest alternative to F2mtz?
> 
> regards,
> Ameya
> National chemical laboratory, Pune, India

[ccp4bb] Senior Principal Scientist Position at Sanofi US

2017-10-06 Thread Yu Qiu 
Senior Principal Scientist, Protein Engineering, Biologics Research
Sanofi 
Framingham, MA, US

(Formerly Sanofi Genzyme)
Apply here:
https://sanofi.wd3.myworkdayjobs.com/en-US/Sanoficareers/job/Framingham-MA/Senior-Principal-Scientist--Protein-Engineering--Biologics-Research_R16366?src=SNS-10723=Linkedin

Job description:
Sanofi tirelessly continues on its path towards becoming a world-class 
biologics organization and it is expanding the capabilities in this area. 
Global Biologics Research platform is one of the key cornerstones of this 
ambition, through its mission and key objectives to discover, design and 
generate novel biologics for research portfolio, and to develop and implement 
innovative state-of-the-art technologies. In order to further strengthen our 
Biologics Research technology powerhouse, we are seeking exceptional talents 
with strong background in biologics and highly innovative and creative mindset.

A highly motivated candidate is sought to join the Protein Engineering team 
with the US Sanofi Biologics Research organization. The individual will join 
and lead our crystallography efforts for determining the structures of complex 
biologics formats, including multi-specific antibody antigen complexes, and 
carrying out structure-based analysis and designs. The individual will oversee 
a small team of PhD scientists working on X-ray crystallography, determining, 
analyzing and interpreting the structures to assist protein engineering 
efforts. The individual will work with project teams to assess and address 
sequence and structure-functions issues, and apply structure-based analysis and 
designs to improve therapeutic index of our Biologics R pipeline. The 
individual will have strong communication skills to collaborate effectively 
with team members and collaborators in protein expression, modification, and 
characterization areas, and to represent structure biology and protein 
engineering teams in project meetings and collaborations. This position will 
report to Head of Protein Engineering in US Sanofi Biologics Research.

Qualifications

Ph.D. in protein crystallography or equivalent with a minimum of 10 years of 
relevant work experience, in either academic or Biotech and Pharmaceutical 
companies. Proven in-depth knowledge and expertise in protein structural 
biology demonstrated preferably through principal authorship in peer-reviewed 
publications. Specifically, candidates must have extensive experience in 
protein complex expression, purification, crystallization, data collection and 
structure determination with strong protein chemistry skills. Prior experience 
on antibody structure determination and structure-based design is highly 
desired. The candidate also needs to have excellent communication and 
presentation skills, and work well in a team and matrix environment. Prior 
management experience is preferred.
Sanofi is a global healthcare leader focused on patients' needs, engaged in the 
research, development, manufacturing and marketing of therapeutic solutions 
focused on patients' needs. Sanofi has core strengths in diabetes solutions, 
human vaccines, innovative drugs, consumer healthcare, emerging markets and 
Sanofi Genzyme.

At Sanofi, our ambition is to be an integrated global healthcare company, 
focused on patients' needs. Much more than just a leading pharmaceutical 
company, Sanofi is committed to transforming scientific innovations into 
solutions and services that protect health, enhance life, and respond to the 
needs of the 7 billion people in the world. We trust our ambition to guide and 
inspire us as we work to create a future with optimal health and wellness for 
everyone.
https://www.linkedin.com/jobs/view/423614880/

[ccp4bb] EBI moving to HTTPS access

2017-10-06 Thread John Berrisford 
Hi CCP4BB 

 

In December all access to EBI will be over HTTPS only. 

Users who visit the www.ebi.ac.uk   web page over HTTP
will be seamlessly redirected to HTTPS.

However, we are aware that this redirect may cause issues for programmatic
access and you may find that you have to change any programmatic requests to
HTTPS. 

 

I'm really sorry for the short notice, but we only received very short
notice of the change. 

 

Regards

 

John

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  pdbe.org

 
http://www.facebook.com/proteindatabank

  http://twitter.com/PDBeurope

Re: [ccp4bb] Creating a covalent bond

2017-10-06 Thread Robbie Joosten 
Dear Jiyong Su,

The go-to program for this is currently jligand from CCP4. To define a link you 
load both compounds (ASP and your thing), delete the leaving atoms (don't 
forget the hydrogens), define the bond (right click to change the bond order if 
needed). Then you can save the definition (there is a refinement step here) as 
mmCIF and you also get a template LINK record to put in  your PDB file.

Cheers,
Robbie 

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Jiyong Su
> Sent: Friday, October 06, 2017 14:19
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Creating a covalent bond
> 
> Dear CCP4 BB,
> 
> We solved one co-crystal structure of a protein and a compound. We found
> this compound could covalently modify an asparate residue of this protein. A
> covalent bond formed between a oxygen atom of Asp carboxyl group and a
> carbon atom of that compound. Does anyone knows how to draw a covalent
> bond between the oxygen atom and the carbon atom and refined it? We
> tried coot, pymol and chimera, but failed. Thank you in advance!
> 
> Best regards,
> 
> Jiyong Su

Re: [ccp4bb] Creating a covalent bond

2017-10-06 Thread Eleanor Dodson 
If you feed it into REFMAC with  review restraints mode - it will create a
bond between two atoms within bonding distance and write a LINKR record
into the output PDB.

You can then use that coordinate file and the LINK dictionary to refine the
model

There are other ways using the up-to-the-moment COOT.

Eleanor Dodson



On 6 October 2017 at 13:18, Jiyong Su  wrote:

> Dear CCP4 BB,
>
> We solved one co-crystal structure of a protein and a compound. We found
> this compound could covalently modify an asparate residue of this protein.
> A covalent bond formed between a oxygen atom of Asp carboxyl group and a
> carbon atom of that compound. Does anyone knows how to draw a covalent bond
> between the oxygen atom and the carbon atom and refined it? We tried coot,
> pymol and chimera, but failed. Thank you in advance!
>
> Best regards,
>
> Jiyong Su
>
>

Re: [ccp4bb] Creating a covalent bond

2017-10-06 Thread Christian Roth 
The easy way is Coot

Extensions Link two atoms which should create a Link record in the pdb.

I think the better way is use jligand which creates a full dictionary
describing the particular link with proper restraints.
Load your ligand,  load the Asp monomer
link the two atoms in question
create the dictionary (Regularize link)
add the link record created by jligand to your pdb
use the dictionary in subsequent refinements
You might have to combine the link library with your dictionary of your
ligand using the merge lib task (I'm not sure right now if jligand
automatically creates the dictionary for the ligand as well)

Cheers

Christian


On Fri, Oct 6, 2017 at 1:18 PM, Jiyong Su  wrote:

> Dear CCP4 BB,
>
> We solved one co-crystal structure of a protein and a compound. We found
> this compound could covalently modify an asparate residue of this protein.
> A covalent bond formed between a oxygen atom of Asp carboxyl group and a
> carbon atom of that compound. Does anyone knows how to draw a covalent bond
> between the oxygen atom and the carbon atom and refined it? We tried coot,
> pymol and chimera, but failed. Thank you in advance!
>
> Best regards,
>
> Jiyong Su
>
>

[ccp4bb] Creating a covalent bond

2017-10-06 Thread Jiyong Su 
Dear CCP4 BB,


We solved one co-crystal structure of a protein and a compound. We found this 
compound could covalently modify an asparate residue of this protein. A 
covalent bond formed between a oxygen atom of Asp carboxyl group and a carbon 
atom of that compound. Does anyone knows how to draw a covalent bond between 
the oxygen atom and the carbon atom and refined it? We tried coot, pymol and 
chimera, but failed. Thank you in advance!


Best regards,


Jiyong Su

[ccp4bb] Off topic: Anyone still using Oxford Cryosystems Cryostream 600 series?

2017-10-06 Thread Ana Luísa Moreira de Carvalho 
Dear colleagues,


Anyone still using Oxford Cryosystems Cryostream 600 series?
We would like to know if there is interest in a computer program to control 
these units via a rs232 connection. We are implementing this in our home source.

For data collection, the program allows automated shutdown if no new images are 
collected for a specified period.

The data collection software in our home source has this functionality but it 
does not support these old units.  Since our controller is working fine, and is 
quite robust, we have no reason to replace it.

With this program we can leave data collection running overnight and the cryo 
shuts down automatically when finished. 

Please, let me know if this would be a useful feature to add to your X-ray 
facility. Reply privately, if you prefer.
Thanks and best wishes
Ana Luisa



Research Assistant Professor at UCIBIO@REQUIMTE-FCT-NOVA
***
Biologia Estrutural - Cristalografia de Raios-X (Gab 6.34)
Dep. Quimica, FCT-NOVA
2829-516 Caparica
Portugal
Phone: 00351212948300 (ext: Gab: 10940; Lab: 10962; X-ray Lab: 10915)
Fax: 00351212948550
http://docentes.fct.unl.pt/almc
http://sites.fct.unl.pt/xtal
https://www.facebook.com/XtalNOVA/
***
Single Crystal X-ray Structure Determination Service: 
http://www.dq.fct.unl.pt/en/single-crystal-x-ray-structure-determination



Research Assistant Professor at UCIBIO@REQUIMTE-FCT-NOVA
***
Biologia Estrutural - Cristalografia de Raios-X (Gab 6.34)
Dep. Quimica, FCT-NOVA
2829-516 Caparica
Portugal
Phone: 00351212948300 (ext: Gab: 10940; Lab: 10962; X-ray Lab: 10915)
Fax: 00351212948550
http://docentes.fct.unl.pt/almc
http://sites.fct.unl.pt/xtal
https://www.facebook.com/XtalNOVA/
***
Single Crystal X-ray Structure Determination Service: 
http://www.dq.fct.unl.pt/en/single-crystal-x-ray-structure-determination

Re: [ccp4bb] HKL to mtz

2017-10-06 Thread Phil Evans 
Note that Combat and Scala are both obsolete

ccp4i2 has useful tasks for importing unmerged data (Data reduction) or merged 
data (Import merged data) from various formats

Phil


> On 6 Oct 2017, at 07:05, Ruud Hovius  wrote:
> 
> Hello, 
> 
> Using Combat followed by Scala in CCP4 works well with as input the .HKL from 
> XDS.
> or, Pointless-Aimless-Ctruncate with which it is also easy to exclude batches 
> .
> 
> best greetings, Ruud
> 
> On 6/10/17 05:01, ameya benz wrote:
>> Hi,
>> 
>> I want to convert HKL file to mtz. I tried using F2mtz but somehow the 
>> output mtz is not working. What parameters should I set during conversion. 
>> Or can anyone suggest alternative to F2mtz?
>> 
>> regards,
>> Ameya
>> National chemical laboratory, Pune, India
> 
> -- 
> 
> Ruud Hovius
> EPFL SB ISIC LIP
> BCH 4209
> CH-1015 Lausanne
> +41-21-693-9442
> 
> http://lip.epfl.ch

Re: [ccp4bb] HKL to mtz

2017-10-06 Thread Graeme Winter 
pointless -c xdsin XDS_ASCII.HKL hklout xds_ascii.mtz
aimless hklin xds_ascii.mtz hklout merged.mtz << eof
scales unity
eof

should do it - is how I usually do this & it also gives a nice merging report...

Best wishes Graeme




From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of ameya benz 
[ameyab...@gmail.com]
Sent: 06 October 2017 04:01
To: ccp4bb
Subject: [ccp4bb] HKL to mtz

Hi,

I want to convert HKL file to mtz. I tried using F2mtz but somehow the output 
mtz is not working. What parameters should I set during conversion. Or can 
anyone suggest alternative to F2mtz?

regards,
Ameya
National chemical laboratory, Pune, India

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Re: [ccp4bb] HKL to mtz

2017-10-06 Thread Eleanor Dodson 
Is your HKL file unmarked scaled data from XDS?
If so read it directly into the Data Reduction task (pointless / aimless
truncate) to produce a merged mtg file.

If the data is already merged, then f2mtz can convert it to an mtg

Eleanor

On 6 October 2017 at 07:05, Ruud Hovius  wrote:

> Hello,
>
> Using Combat followed by Scala in CCP4 works well with as input the .HKL
> from XDS.
> or, Pointless-Aimless-Ctruncate with which it is also easy to exclude
> batches .
>
> best greetings, Ruud
>
> On 6/10/17 05:01, ameya benz wrote:
>
> Hi,
>
> I want to convert HKL file to mtz. I tried using F2mtz but somehow the
> output mtz is not working. What parameters should I set during conversion.
> Or can anyone suggest alternative to F2mtz?
>
> regards,
> Ameya
> National chemical laboratory, Pune, India
>
>
> --
>
> Ruud Hovius
> EPFL SB ISIC LIP
> BCH 4209
> CH-1015 Lausanne+41-21-693-9442 <+41%2021%20693%2094%2042>http://lip.epfl.ch
>
>

[ccp4bb] Beamtime @ SLS

2017-10-06 Thread Meitian Wang 
===
SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS
===

Proposal application deadline: Sunday, October 15, 2017

Periods:
January 1, 2018 - June 30, 2018 (Normal / Test proposals)
January 1, 2018 - December 31, 2019 (Long-term proposals)

Proposal submission:
http://www.psi.ch/sls/px-beamlines-call-for-proposals 


Travel support is available via CALIPSOplus (http://www.calipsoplus.eu/ 
)

What's New (http://www.psi.ch/sls/pxi/pxi ) 
- X06SA
Fast beam size changing from 5 x 5 to 80 x 80 micron^2, one-micron beam 
available
EIGER 16M detector (133 Hz)
Continous grid scan (100Hz)
Serial data collection GUI (CY+)
- X06DA
Rapid access mode for experimental phasing, especially native-SAD 
(contact directly vincent.olie...@psi.ch )
- Sample changer
30 second sample exchange time

Beamline characteristics and features
X06SA Beamline (http://www.psi.ch/sls/pxi/pxi )
X06DA Beamline (http://www.psi.ch/sls/pxiii/pxiii 
)
X10SA Beamline (http://www.psi.ch/sls/pxii/pxii 
)

Best regards,

The MX group at SLS
__
Meitian Wang
Swiss Light Source at Paul Scherrer Institut
CH-5232 Villigen PSI - http://www.psi.ch/sls/ 
Phone: +41 56 310 4175

Re: [ccp4bb] HKL to mtz

2017-10-06 Thread Ruud Hovius 

Hello,

Using Combat followed by Scala in CCP4 works well with as input the .HKL 
from XDS.
or, Pointless-Aimless-Ctruncate with which it is also easy to exclude 
batches .


best greetings, Ruud

On 6/10/17 05:01, ameya benz wrote:

Hi,

I want to convert HKL file to mtz. I tried using F2mtz but somehow the 
output mtz is not working. What parameters should I set during 
conversion. Or can anyone suggest alternative to F2mtz?


regards,
Ameya
National chemical laboratory, Pune, India


--

Ruud Hovius
EPFL SB ISIC LIP
BCH 4209
CH-1015 Lausanne
+41-21-693-9442
http://lip.epfl.ch