[ccp4bb] opening for Postdoctoral fellow - Pfizer Structural and Molecular Sciences

[Calabrese, Matthew]

* The successful candidate will join the Groton Structural and 
Molecular Sciences group which has extensive expertise in the gene to structure 
pipeline, in addition to biophysics and chemical biology.  Our mission is to 
provide integrated molecular insights into drug targets and target-ligand 
interactions to impact drug discovery efforts across multiple therapeutic areas.
*
The selected candidate will, in collaboration with others, perform research to 
understand protein-protein and protein-ligand interactions and the impact of 
ligand binding on target ubiquitination and degradation.  Responsibilities will 
include design of appropriate experiments, collecting and analyzing data, 
working independently in a laboratory environment in addition to performing 
other related duties, tasks and responsibilities as required.  The applicant 
training may/will include mammalian cell culture, molecular biology, protein 
expression and purification, protein-ligand binding studies, in vitro assay 
development, and x-ray crystallography.  These efforts will be part of a larger 
team working to advance treatments for multiple diseases, as such you will have 
the opportunity to learn techniques from experienced colleagues throughout the 
Groton Structural and Molecular Sciences group and gradually build a broad 
understanding of other biology and chemistry disciplines involved in drug 
discovery.  This position offers an opportunity to help contribute to the 
understanding of a serious disease and will place the successful candidate into 
an environment rich with training opportunities, access to high level 
scientific equipment and excellent support for research materials.  You will be 
expected to present your results at an external meeting and publish your 
findings in high impact journals.

Basic Qualifications
oRecent PhD in Biochemistry or a related field, or within 6 months of 
completion, and a track record of quality first authored publications
oThe successful candidate should have the desire and experience to carry 
out independent experiments and the creativity and drive to tackle challenging 
problems.  Successful candidates will possess excellent communication and 
collaboration skills to succeed in a team environment.
o
Matthew Calabrese
Senior Principal Scientist - Structural Biology and Biophysics
matthew.calabr...@pfizer.com

Re: [ccp4bb] refmac output

[Diana Tomchick]

Yes, I agree! This (“Please look at my structure, and here are my files from 
the last cycle of refinement") happens to me almost every week. :)

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Aug 1, 2017, at 10:48 AM, James Holton  wrote:

As someone who uses those "superfluous" columns all the time, I would like to 
chime in in favor of keeping the default output columns of refmac.  If only I 
had a nickle for every time someone asked me to "look at" a structure and only 
gave me the output files of refinement.  Kind of ties your hands.

I have always been a fan of erring on the side of providing information in 
output files.  How hard is it to delete something? How hard is it to get it 
back after you deleted it?

My two cents,

-James Holton
MAD Scientist

On 7/31/2017 8:57 AM, Edwin Pozharski wrote:
> I know space is cheap these days, but is there a reason for Refmac to 
> generate all those extra columns in the output mtz file?  Refmac (as well as 
> phenix.refine and buster-tnt) output mtz file is almost always used for only 
> one purpose - look at the map in coot.  You only need 4 columns for that, not 
> 14.  Other columns are useful for testing, but why not make them optional?
>
> This would certainly be a low priority - one can easily delete extra columns 
> using, say, sftools.
>
> Cheers,
>
> Ed.
>
> ---
> Hurry up, before we all come to our senses!
> Julien, King of Lemurs
>




UT Southwestern


Medical Center



The future of medicine, today.

Re: [ccp4bb] refmac output

[James Holton]

As someone who uses those "superfluous" columns all the time, I would 
like to chime in in favor of keeping the default output columns of 
refmac.  If only I had a nickle for every time someone asked me to "look 
at" a structure and only gave me the output files of refinement.  Kind 
of ties your hands.


I have always been a fan of erring on the side of providing information 
in output files.  How hard is it to delete something? How hard is it to 
get it back after you deleted it?


My two cents,

-James Holton
MAD Scientist

On 7/31/2017 8:57 AM, Edwin Pozharski wrote:
I know space is cheap these days, but is there a reason for Refmac to 
generate all those extra columns in the output mtz file?  Refmac (as 
well as phenix.refine and buster-tnt) output mtz file is almost always 
used for only one purpose - look at the map in coot.  You only need 4 
columns for that, not 14.  Other columns are useful for testing, but 
why not make them optional?


This would certainly be a low priority - one can easily delete extra 
columns using, say, sftools.


Cheers,

Ed.

---
Hurry up, before we all come to our senses!
Julien, King of Lemurs

[ccp4bb] drawing of peptide interaction

[chemocev marker]

Hi
I wanted to draw a peptide interaction in the catalytic site together with
side chain of the enzyme. What is a good program to do that, or web based
service. I see the LIGPLOT and I am wondering if there are some other
alternatives of that.

best

Jiri

Re: [ccp4bb] weird diffraction pattern

[James Holton]

Hello Tang,

1) For MR, you might want to try a range of homologs, or even a stack of 
overlapping homologs. A normal modes server like elNemo might also help 
if it can predict the "bend" your molecule undergoes upon binding.  A 
long shot perhaps, but stranger things have happened.  You also might be 
able to find the DNA by molecular replacement.


2) radiation damage increases with photons/area, not time.  So no matter 
what your degrees/image you want the total shuttter-open time at the end 
of the data set to be below the damage limit of interest.  A little web 
app I made once might help: http://bl831.als.lbl.gov/xtallife.html .  
These days, there is no reason not to know how long your crystal will 
last before you push "collect", and it is definitely worth knowing.


-James Holton
MAD Scientist

On 7/28/2017 12:21 AM, Tang Chenjun wrote:

Hi,

Thanks to all who gave me suggestions concerning the weird diffraction pattern 
and I really appreciate it that Kay Diederichs help me processing my data set 
and answer my questions. Although the data set can be processed using HKL3000, 
XDS without problems, the Rwork/Rfree values are still above 0.5 after 
molecular replacement. There can be several reasons.
1) The structure change a lot after binding DNA, so it is not possible to find 
a solution using molecular replacement.
2) Strong radiation damage and 1.0 degree image widths prevent good integration 
results. It may be better to use 0.1 degree image widths.
3) Streaky spots appearing in certain directions because of anisotropy or 
lattice translocation disorder, or one very large unit cell dimension lying 
along the X-ray beam may also have an affect on data processing.

Now I am optimizing the crystals to address these problems.

Best wishes and thanks again for your help,

Chenjun Tang

[ccp4bb] PDBepisa

[Careina Edgooms]

 HelloI have two questions if anyone can help:1. Does anyone know how PDBe Pisa 
calculate if the residues interact? I can't find an explanation for this.
2. Also, I want to do SAXS on a liquid sample using a rigaku smartlab x-ray 
diffractometer. It is set up for powder and the software they use is Globalfit 
or Nano solver. Does anyone know if I can use this to analyse liquid sample?
Thanks in advanceCareina