[ccp4bb] Issues in diffraction image export compatible to iMosflm

[Vyankatesh Rajmane]

Dear all,
We have collected diffraction data on a Rigaku FR-X machine with a
HyPix-6000HE detector. The images are in .rod_img format. We are trying to
export the data in iMosflm compatible format using the options available in
CrysAlisPro RED software provided by Rigaku. But the images generated show
vertical strips instead of diffraction spots which gives error in
processing. Can anyone suggest a method to convert the .rod_img images in
iMosflm compatible format. Thank you!

-- 
 Vyankatesh Rajmane
E-mail: vyankates...@gmail.com



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[ccp4bb] PNCC Screening Access Mechanism

[Kjirsten Wheeler]

Hello CryoEM Researchers,
Pacific Northwest CryoEM Center is offering a mechanism developed to help 
laboratories with limited or no cryo-EM resources enter the field of cryo-EM. 
PNCC's "Screening Access Mechanism" will provide users on-site access to 
state-of-the-art cryo-EM resources and expertise to carry out sample 
preparation and optimization under close supervision of trained cryo-EM 
specialists.

Our goal is to help users identify cryo-grid conditions that will be successful 
for transitioning to data collection activities provided by PNCC's General 
Access mechanism or to establish the technical feasibility and provide guidance 
on the next states of the project. We hope this new mechanism will enable 
investigators lacking access to local cryo-EM resources and help jump-start 
investigators interested in entering the field of cryo-EM.

For more information about our "Screening Access Mechanism", go 
here.
 Applications are accepted on a monthly basis, with the next deadline for this 
proposal type being November 1st, 2023 at 11:59pm (Pacific) in our portal here. 
Step-by-step instructions on how to submit a proposal to PNCC can be found 
here.



We request your help by disseminating this information to colleagues who may be 
interested in engaging in the field of cryo-EM
_
Kjirsten Wheeler
PNCC Administrative Coordinator
Pacific Northwest Cryo-EM Center
a PNNL and OHSU affiliation
Website
PNCC 
Twitter

wheel...@ohsu.edu




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[ccp4bb] How can I refine the occupancy with Refmac? Revisited

[Marian Oliva]

Dear list,

In my structure there are some residues in alternative conformations that I 
would like to refine. I have mostly run Phenix for refinement but recently, I 
have switched to Refmac and since I have no much of experience I dig into the 
ccp4 archive and found some tips from Eleanor Dodson and James Holton.

I am currently running refmac from ccp4i2 (ccp4-8.0.015). In this interface, 
when you specify partial occupancies group, a table appears where you can set 
Group ID, chain, from residue, to residue, (atom) and, (alt). 

In my case, Group ID is always 1 and I cannot change it into a different value, 
which is contrary to what James shared in his examples (shown below)

# typical lysozyme
% refmac_occupancy_setup.com  193l.pdb
occupancy refine
occupancy group id 1 chain A residue 1 alt A
occupancy group id 2 chain A residue 1 alt B
occupancy group id 3 chain A residue 59 alt A
occupancy group id 4 chain A residue 59 alt B
occupancy group id 5 chain A residue 86 alt A
occupancy group id 6 chain A residue 86 alt B
occupancy group id 7 chain A residue 109 alt A
occupancy group id 8 chain A residue 109 alt B
occupancy group alts complete  1 2
occupancy group alts complete  3 4
occupancy group alts complete  5 6
occupancy group alts complete  7 8

My first questions are
- If you do not introduce any value in the table, can refmac recognize 
alternative conformations from the input pdb and refine them?
- Could it be that there issome issue in my setup for running Refmac? No idea 
about where the mistake is. 

Any help will be really appreciate.

Best,
Marian

Marian Oliva
CSIC-Centro de Investigaciones Biológicas Margarita Salas
9, Ramiro de Maeztu
28040-Madrid (Spain)

phone: 0034 91 1097301
e-mail: mar...@cib.csic.es

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