Oh wonderful, that is exactly what I was looking for, I will test it now! Thanks Randy! Cheers Oli

On Nov 13, 2023, at 10:30 AM, Randy John Read wrote:

Hi Oli,

The relatively new EM_placement docking tool (phenix.voyager.em_placement) has an option to refine the voxel size as part of the likelihood-based rigid-body refinement step, and it seems to work pretty well. At the moment, this has to be done as part of a docking search, but I’m planning to implement a rigid-body refinement option for previously-placed models, which might be useful in some circumstances.

Best wishes,

Randy

...

On 13 Nov 2023, at 13:42, Oliver Clarke wrote:

Hi,

In cryoEM, the pixel size is often not known with certainty, and we need to calibrate it by measuring the real space correlation of a reference crystal structure of a component at different nominal pixel sizes.

Currently we do this manually, using `fitmap` in UCSF Chimera, but given the sophisticated set of tools in Phenix for fitting atomic models and analyzing real space correlations, I was wondering if a tool in Phenix already exists to do this, or whether there would be any interest in adding such a tool at some point?

Cheers Oli _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

Yes, that’s the right option! It doesn’t allow you to specify a starting scale value, which defaults to 1. That might be a useful option for cases where the initial docking fails because the scale is too far from the correct value. My impression is that this used to be a bigger problem in the past, but that microscopes are generally calibrated reasonably well these days. Best wishes, Randy

On 13 Nov 2023, at 15:45, Oliver Clarke wrote:

Is that the option "refine_cell_scale"? Or is there another option I am overlooking

Cheers Oli

...

On Nov 13, 2023, at 10:41 AM, Oliver Clarke wrote:

Oh wonderful, that is exactly what I was looking for, I will test it now! Thanks Randy!

Cheers Oli

...

On Nov 13, 2023, at 10:30 AM, Randy John Read wrote:

Hi Oli,

The relatively new EM_placement docking tool (phenix.voyager.em_placement) has an option to refine the voxel size as part of the likelihood-based rigid-body refinement step, and it seems to work pretty well. At the moment, this has to be done as part of a docking search, but I’m planning to implement a rigid-body refinement option for previously-placed models, which might be useful in some circumstances.

Best wishes,

Randy

...

On 13 Nov 2023, at 13:42, Oliver Clarke wrote:

Hi,

In cryoEM, the pixel size is often not known with certainty, and we need to calibrate it by measuring the real space correlation of a reference crystal structure of a component at different nominal pixel sizes.

Currently we do this manually, using `fitmap` in UCSF Chimera, but given the sophisticated set of tools in Phenix for fitting atomic models and analyzing real space correlations, I was wondering if a tool in Phenix already exists to do this, or whether there would be any interest in adding such a tool at some point?

Cheers Oli _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk