[ccp4bb] CBMS Structural Biology Workbench - June 3 to 6, 2024

[Stojanoff, Vivian]

Dear All, Share with new members in your group

You are cordially invited to join the CBMS Structural Biology Workbench, June 3 
to 6. All practical sessions will be held in-person. To participate  in-person, 
participants need to register for the workbench and have an active BNL Guest 
Appointment.

To register:  https://www.bnl.gov/cbmsworkbench/index.php   Choose from remote 
or in-person registration. Remote registration is free.

In-person participation is limited and requires an Active Brookhaven Guest 
Appointment.  In-person participation ONLY if you have an active BNL Guest 
Appointment.

CBMS Team




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[ccp4bb] REMINDER >>> CBMS Lecture Series - Narayanasami Sukumar - April 17

[Stojanoff, Vivian]

You are cordially invited to join  the Center for Biomolecular Structure 
Lecture Series ………..





 Narayanasami Sukumar


Cornell University


NE CAT, Advance Photon Source





WEDNESDAY, April 17, 13:30 (EDT)



"An in-depth study on electron transfer mechanism in cupredoxins"



Register in advance for this meeting:


https://bnl.zoomgov.com/meeting/register/vJIsdOyppjIuE9myS_Utu_WtaGoyVnNkXBI



   Time conversion Link: 
https://www.worldtimebuddy.com/


 ABSTRACT: Electron transfer (ET) through and between proteins is a frequently 
occurring biological process in both prokaryotes and eukaryotes. Understanding 
the principle behind the ET will help to understand the important biological 
processes like respiration and photosynthesis. The major focus of the talk 
would be on the type I copper protein, amicyanin which accepts electrons from 
quinone cofactor of methylamine dehydrogenase and donates them to a c-type 
cytochrome over long distance. Along with amicyanin, the talk would cover the 
following: (a) another type I copper protein azurin in complex with 
quinoprotein aromatic amine dehydrogenase, (b) role of dynamics in crystalline 
state, analyzed by joint x-ray and neutron study, (c) mutational studies on 
amicyanin, and (d) charge density/ultra-high-resolution studies on amicyanin 
which are currently in progress. Several instances where synchrotron 
crystallography played important role in elucidating catalytic mechanism will 
be discussed.



==



Vivian Stojanoff, PhD

Education, Training, Outreach

User Program

p 1(631) 344 8375

e lifescie...@bnl.gov

w https://www.bnl.gov/ps/lifesciences/



Address:

Center for Biomolecular Structure

National Synchrotron Light Source II

Building 745

Brookhaven National Laboratory

Upton NY 11973





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Re: [ccp4bb] Request for assistance with structure solution

[Yehudi BLOCH]

Dear Adewumi

I'm afraid the 85% complete dataset is a contaminant as well.
PDB 2r6s and related entries for E.coli Gab protein have near identical unit 
cell parameters. The autoprocessed (?) .mtz file you attached also solves with 
this E.coli protein.
I suppose that if you rerun XDS with the given unit cell parameters things 
should process.

Best
Yehudi



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[ccp4bb] error when running pandda.inspect

[Nicolas Foos]

Dear community,

I am trying to run panDDA. As first, I am simply trying to follow the 
tutorial.


I have an issue with pandda.inspect:

"INFO:: There are 1 command line scripts to run
/storage/software/ccp4/ccp4-8.0/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
calling run_script() for file 
/storage/software/ccp4/ccp4-8.0/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
debug:: run_script() on 
/storage/software/ccp4/ccp4-8.0/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py
Running python script 
/storage/software/ccp4/ccp4-8.0/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py

Traceback (most recent call last):
  File "", line 1, in 
  File 
"/storage/software/ccp4/ccp4-8.0/bin/../lib/python3.7/site-packages/pandda/inspect/__init__.py", 
line 1, in 

    import giant.logs as lg
ImportError: No module named giant.logs"

So I tried to fixed it myself, without success up to now. Maybe I am 
missing something obvious.


I did search on the ccp4bb archive. Someone had exactly the same issue. 
But I couldn't find any answer.


If someone could help me.

Have a nice day.

Nicolas

--
Nicolas Foos PhD - ARISE fellow
https://orcid.org/-0003-2331-8399
   
EMBL Grenoble, McCarthy Team

71 av. des Martyrs,
38000 Grenoble FRANCE
   
+33 4 57 42 84 67




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Re: [ccp4bb] Staff position at UCSC

[Vitor Hugo Balasco Serrão]

Dear Structural Biology community,

Just a friendly reminder that we are still seeking applications for the new
staff scientist position (specialist series) available within the
Department of Chemistry and Biochemistry at UC Santa Cruz.

The scientist will work with users of the Biomolecular Cryo-Electron
Microscopy Facility and oversee, process, and analyze data.
There will be opportunities to collaborate with UCSC faculty on determining
macromolecular structures through single particle cryo-EM, subtomogram
averaging, and micro electron diffraction approaches.
Additionally, we envision that the scientist will lead and instruct
researchers in computational structural biology methods, including deep
learning approaches.

Please be aware that remote work arrangements may be considered.

For more information and to apply, see https://recruit.ucsc.edu/JPF01703

Seth Rubin, Professor of Chemistry and Biochemistry
Vitor Serrão, UCSC cryo-EM Facility manager
Department of Chemistry and Biochemistry
University California - Santa Cruz
1156 High St - Santa Cruz, CA - 95060
Phone: +1 831/4007378
vbala...@ucsc.edu

On Fri, Mar 22, 2024 at 12:39 PM Vitor Hugo Balasco Serrão <
vbala...@ucsc.edu> wrote:

> Dear Structural Biology community,
>
> We are excited to announce a new staff scientist position (specialist
> series) available within the Department of Chemistry and Biochemistry at UC
> Santa Cruz.
>
> The scientist will work with users of the Biomolecular Cryo-Electron
> Microscopy Facility and oversee, process, and analyze data. There will be
> opportunities to collaborate with UCSC faculty on determining
> macromolecular structures through single particle cryo-EM, subtomogram
> averaging, and microelectron diffraction approaches.
> Additional, we envision that the scientist will lead and instruct
> researchers in computational structural biology methods, including deep
> learning approaches.
>
> Please be aware that remote work arrangements may be considered.
>
>
> For more information and to apply, see https://recruit.ucsc.edu/JPF01703
>
> Seth Rubin, Professor of Chemistry and Biochemistry
>
> Vitor Serrão,
> UCSC cryo-EM Facility manager
> Department of Chemistry and Biochemistry
> University California - Santa Cruz
> 1156 High St - Santa Cruz, CA - 95060
> Phone: +1 831/4007378
> vbala...@ucsc.edu
>



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[ccp4bb] ÄktaXpress to PC adapter : Off topic

[Deepak Deepak]

Dear CCP4 community,

We recently acquired some ÄktaXpress systems from our neighboring lab, but
unfortunately, we are missing the essential *adapter cable (Uninet-CAN)*.
Does your lab have this Äktaxpress cable but don't need any more,  we would
greatly appreciate your assistance.

As a point of reference, Cytiva offers this cable for approximately *3,000
USD*

1
.
Unfortunately, another company that used to provide these cables at a lower
cost now has contract agreements with Cytiva, preventing them from selling
directly to individual customers.

If you have any leads or can help us obtain the Uninet-CAN adapter cable,
that would be greatly appreciated.

Apologize for the off-topic nature of this request and sincerely appreciate
your support.

Many thanks,

Deepak



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