[ccp4bb] SEC and MALS

[Natesh Ramanathan]

Dear  Friends,

Can you share your experience with examples of MALS giving lower
molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg.
Dimer),  for the same protein sample?

  If you have/know any published paper, can you please point me to that
reference paper or send me the paper?

Many thanks.
Best regards,
Natesh


-- 
--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Assistant Professor,
School of Biology,
Indian Institute of Science Education and Research Thiruvananthapuram
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

nat...@iisertvm.ac.in
http://www.researcherid.com/rid/C-4488-2008
ORCID: http://orcid.org/-0002-1145-5962
https://publons.com/author/1520837/ramanathan-natesh#profile
http://faculty.iisertvm.ac.in/natesh

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[ccp4bb] RFP for Drug Discovery - In Silico Small Molecule Screening Awards

[Nick DeHaan]

Hi CCP4BB Community,

I’m excited to announce that the next round of the Atomwise AIMS Awards
program is now accepting proposals! The award program provides in silico
small molecule screening as well as compounds and is open to all non-profit
research institutions, including international applicants.

This cycle, we are also excited to offer a few awards that provide in-kind
support up to $20K to subsidize assay work, in addition to screening and
compounds. Please feel free to share this opportunity with your colleagues
and collaborators. You can find more info and apply online at
http://bit.ly/33Y1zVp.

The goal of the AIMS Awards program is to help researchers discover new
molecular tool compounds or start drug discovery programs. Atomwise has
worked with over 200 research institutions via this program, including
Duke, Tulane, University of Toronto, and DNDi.

Please don’t hesitate to reach out with any questions. You can contact me
directly at n...@atomwise.com.

Best,
Nick

-- 
Nick DeHaan, MsE
*Partnering Executive*
*Atomwise*  | *Better Medicines Faster*
ᐧ

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Re: [ccp4bb] SeMet data

[Nukri Sanishvili]

Hi Lindsey,
Obviously, one would need a lot more information to properly diagnose the
problem and I am sure much smarter people them me will ask you for that.
But just to move the task by couple of steps, I want to point out couple of
things.
1. Trivial question: did you have the anomalous option turned on during
data processing? (Just like from the IT help - is your computer turned on?)
2. How much data did you collect for each half of the inverse beam
geometry? If you have enough, try phasing with only one half. When done
properly, inverse beam experiment is great but it can easily get tricky
introducing systematic errors and thus swamping anomalous signal.  If you
redo the inverse beam, use little wider wedges, say, 5-10 degrees.
3. I thought an example of diffraction image would not give any useful
information but... Judging by how smooth the background is on your Pilatus
image, I am guessing you have used a lot of exposure. Can you calculate how
much dose did you put in your crystal? If you are going to re-do the
experiment, I would suggest reducing the exposure level and collecting more
data.
4. Because you are not showing f' and f" plots, I am guessing that you are
doing SAD. If it fails and you end up redoing your experiment and you have
crystals for it, you might want to try 2-wavelength MAD but for that you
would need to know exactly where is inflection point and collect one of the
datasets there.

Good luck!
Nukri

On Mon, Aug 26, 2019 at 5:45 PM L. Doyle  wrote:

> I have some Seleno-Methionine protein crystals (12 SeMet of 211 amino
> acids, incorporation verified by Mass Spec). I've already collected several
> datasets (ALS BL5.0.2) but I seem to be losing (rejecting?) a lot of
> anomalous signal during data processing. I'm most familiar with HKL2000,
> but I have tried XDS and DIALS auto-processing. Here is a scan:
> https://ibb.co/LZqm33p and here is an example of a frame:
> https://ibb.co/gR3ZR47. Each frame is 0.25° and I'm using inverse beam
> with wedge size 1°. Maybe I need to adjust my collection strategy? All
> previous datasets have been in space group P 21 with dimensions of approx.
> 24.5Å, 85Å, 40Å, 90°, 96.5°, 90°. I'm sure there are additional things I
> can be doing in HKL but I've run out of ideas. Any advice or
> recommendations would be appreciated. Please let me know if you need
> additional information.
>
> Thank you,
> Lindsey
>
> 
>
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>



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[ccp4bb] Postdoc position in San Antonio, Texas

[Yogesh Gupta]

*Postdoctoral Fellow position at UT Health San Antonio, San Antonio, Texas*



The laboratory of Dr. Yogesh Gupta (http://ccri.uthscsa.edu/YGupta.html) at
University of Texas Health Science Center in San Antonio (UT Health San
Antonio™) is seeking a  motivated scientist with strong interest in
structural/mechanistic studies on protein-nucleic acid assemblies in
pediatric cancers. We combine structural/biophyiscal (X-ray, NMR, cryo-EM,
AUC, SAXS), and cell-based methods to address basic mechanistic questions,
and exploit this knowledge for drug discovery.



Our lab is physically located within the Greehey Children’s Cancer Research
Institute  (Greehey CCRI) at UT Health San
Antonio.  We have full access to an extensive array of core institutional
facilities (Biochemistry core
, CIDD ,
Research core labs ) located
within the Department of Biochemistry and Structural Biology, the Joe R.
and Teresa Lozano Long School of Medicine, and Greehey CCRI.  Applicants
with demonstrated experience in protein biochemistry, enzyme kinetics, and
structural biology are preferred. Candidates are expected to possess strong
organizational, interpersonal skills, and ability to work as part of a
team. Candidate should hold (or soon expect to hold) a PhD or equivalent
degree in a related discipline. An ideal candidate should not have >2 years
of prior postdoc experience. Prior experience in X-ray crystallography is
desirable but not required.



Salary is competitive. San Antonio offers affordable cost of living and
there is no state income tax in Texas.



Please visit the websites below to learn more about our work and future
directions –

http://ccri.uthscsa.edu/YGupta.html



If interested in applying, please send a short description of your research
accomplishments, current CV with a list of three (3) references to Dr.
Yogesh Gupta (email: gup...@uthscsa.edu).



The Greehey Children’s Cancer Research Institute is a unique specialized
cancer research center focusing on basic and translational research in
childhood cancer and occupies a state-of-the-art 100,000 sq. foot research
facility on the university’s Greehey Academic and Research Campus.



San Antonio is the nation’s seventh largest city and is located at the edge
of the beautiful Texas Hill County. San Antonio offers a rich,
multi-cultural community, affordable cost of living, excellent weather and
a thriving biomedical industry.



*All Postdoctoral appointments are designated as security sensitive
positions. The University of Texas Health Science Center at San Antonio is
an Equal Opportunity/Affirmative Action Employer including protected
veterans and persons with disabilities.*


-- 
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Assistant Professor of Biochemistry & Structural Biology
PI, Greehey Children's Cancer Research Institute
University of Texas Health Science Center
8403 Floyd Curl Drive, San Antonio, Texas, USA 78229
http://ccri.uthscsa.edu/YGupta.html



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Re: [ccp4bb] SeMet data

[Keller, Jacob]

Why do you think you are rejecting anomalous data? What do the normal 
tell-tales reveal, like anom CC?

JPK

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

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-Original Message-
From: CCP4 bulletin board  On Behalf Of L. Doyle
Sent: Monday, August 26, 2019 6:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] SeMet data

I have some Seleno-Methionine protein crystals (12 SeMet of 211 amino acids, 
incorporation verified by Mass Spec). I've already collected several datasets 
(ALS BL5.0.2) but I seem to be losing (rejecting?) a lot of anomalous signal 
during data processing. I'm most familiar with HKL2000, but I have tried XDS 
and DIALS auto-processing. Here is a scan: 
https://urldefense.proofpoint.com/v2/url?u=https-3A__ibb.co_LZqm33p=DwIFaQ=LU6cRtx0xgB8s29tIz9Olw=eLCg9eJ4Rs_LnxfUWsp7FSxhIEcZYmTSU4Uyq1bRYPI=IY2dWiiG1i1JgjTXPAPNw3-KHrUr53w37DPc7mNTmQk=eA1o_iIowAlvk0KtH7k81LUBeSWfBfCsL7yvZK7KWvM=
  and here is an example of a frame: 
https://urldefense.proofpoint.com/v2/url?u=https-3A__ibb.co_gR3ZR47=DwIFaQ=LU6cRtx0xgB8s29tIz9Olw=eLCg9eJ4Rs_LnxfUWsp7FSxhIEcZYmTSU4Uyq1bRYPI=IY2dWiiG1i1JgjTXPAPNw3-KHrUr53w37DPc7mNTmQk=0Vn8zTPkITbHZuSG2lgAXAZZ5rpwTmNDfRvUjYPvYXs=
 . Each frame is 0.25° and I'm using inverse beam with wedge size 1°. Maybe I 
need to adjust my collection strategy? All previous datasets have been in space 
group P 21 with dimensions of approx. 24.5Å, 85Å, 40Å, 90°, 96.5°, 90°. I'm 
sure there are additional things I can be doing in HKL but I've run out of 
ideas. Any advice or recommendations would be appreciated. Please let me know 
if you need additional information. 

Thank you,
Lindsey



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[ccp4bb] SeMet data

[L. Doyle]

I have some Seleno-Methionine protein crystals (12 SeMet of 211 amino acids, 
incorporation verified by Mass Spec). I've already collected several datasets 
(ALS BL5.0.2) but I seem to be losing (rejecting?) a lot of anomalous signal 
during data processing. I'm most familiar with HKL2000, but I have tried XDS 
and DIALS auto-processing. Here is a scan: https://ibb.co/LZqm33p and here is 
an example of a frame: https://ibb.co/gR3ZR47. Each frame is 0.25° and I'm 
using inverse beam with wedge size 1°. Maybe I need to adjust my collection 
strategy? All previous datasets have been in space group P 21 with dimensions 
of approx. 24.5Å, 85Å, 40Å, 90°, 96.5°, 90°. I'm sure there are additional 
things I can be doing in HKL but I've run out of ideas. Any advice or 
recommendations would be appreciated. Please let me know if you need additional 
information. 

Thank you,
Lindsey



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Re: [ccp4bb] Fo-Fc map in WinCoot

[Raymond Brown]

 Yes that works like magic. Never noticed that little box before. WinCoot is 
jsu wonderful. Hours of endless fun awaits me.

Many thanks

Ray Brown On Monday, August 26, 2019, 10:47:51 AM EDT, Jonathan Cooper 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:  
 
 When you open the map, in the window which comes up there is a little box to 
tick which says "Is difference map?" in the lower left hand corner from memory. 
Then it will display the -ve contours.

Sent from Yahoo Mail on Android 
 
  On Mon, 26 Aug 2019 at 15:34, Raymond Brown wrote:   Hi 
folks,

I notice that WinCoot does not appear to display the negative peaks in Fo-Fc 
difference maps.

Is there a fix for this?

Best

Ray Brown



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Re: [ccp4bb] Fo-Fc map in WinCoot

[Jonathan Cooper]

When you open the map, in the window which comes up there is a little box to 
tick which says "Is difference map?" in the lower left hand corner from memory. 
Then it will display the -ve contours.

Sent from Yahoo Mail on Android 
 
  On Mon, 26 Aug 2019 at 15:34, Raymond Brown wrote:   Hi 
folks,

I notice that WinCoot does not appear to display the negative peaks in Fo-Fc 
difference maps.

Is there a fix for this?

Best

Ray Brown



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[ccp4bb] Fo-Fc map in WinCoot

[Raymond Brown]

Hi folks,

I notice that WinCoot does not appear to display the negative peaks in Fo-Fc 
difference maps.

Is there a fix for this?

Best

Ray Brown



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