[phenixbb] Re: Simulate map from model

On Fri, 4 Apr 2025 15:55:14 +0200 Dear Ricardo, since you still have issues, here is an alternative: you could convert the PDB to SHELXL ins file shelx2map, replace the SFAC commands with electron scattering factors, run SHELXL with LIST 6 and L.S. 0 This would create an fcf-file that you can read into coot. Since Coot speaks crystallography, it creates a crystallographic map from the fcf-file. SFAC commands are listed in the attached file, created with the code on github, https://github.com/CF-CSA/edSFAC/tree/main/atomsMB_AVolkov Best, Tim Ricardo Righetto wrote:

Dear all,

Thanks a lot for your replies!

After playing a bit with the suggested command line programs I decided to follow Robert's suggestion and go the Python way, hoping to gain finer control of the options.

I am using the attached Python script to calculate an exact map from a model, using electron scattering table.

When running, for example, on 4v7t.cif I get a map that looks as follows (orthogonal central slices):

[image: image.png]

And the MRC header as read by IMOD is:

RO image file on unit 1 : fourier_map.mrc Size= 32401 K

Number of columns, rows, sections ..... 320 240 108 Map mode .............................. 2 (32-bit float) Start cols, rows, sects, grid x,y,z ... 0 0 0 108 240 320 Pixel spacing (Angstroms).............. 1.958 1.809 1.941 Cell angles ........................... 90.000 90.000 90.000 Fast, medium, slow axes ............... Z Y X Origin on x,y,z ....................... 0.000 0.000 0.000

Minimum density ....................... 0.0000 Maximum density ....................... 2.5699 Mean density .......................... 0.12004E-01 RMS deviation from mean................ 0.47980E-01 tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0 Space group,# extra bytes,idtype,lens . 19 0 0 0

1 Titles : Some text

With these in mind, I have some questions:

1) If I understand correctly, the map contains exactly one unit cell as defined in the .cif file. How can I choose a different assembly to generate the map from? Say, biological (author-defined) assembly #1?

2) The pixel size is approximately the step I give to maptbx.crystal_gridding() but is not exactly isotropic. How can I enforce it as such?

3) Probably related to the question above, the box size is not cubic, I guess because of the unit cell dimensions. Since most cryo-EM programs expect maps to be cubic and have isotropic pixel sizes, I would like to enforce the final map to be sampled on a cubic grid. How can I do that?

4) Not exactly a question but what might be a bug report. When I use a model that was originally calculated based on a cryo-EM map (PDB entries I tried: 7k00, 7b75) I get the following error because the files have no crystal symmetry defined:

Traceback (most recent call last): File "phenix_simulate_map.py", line 18, in <module> model.setup_scattering_dictionaries(scattering_table="electron") File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Phenix/phenix-1.21-5207/modules/cctbx_project/mmtbx/model/model.py", line 2398, in setup_scattering_dictionaries self.neutralize_scatterers() File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Phenix/phenix-1.21-5207/modules/cctbx_project/mmtbx/model/model.py", line 2821, in neutralize_scatterers xrs = self.get_xray_structure() File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Phenix/phenix-1.21-5207/modules/cctbx_project/mmtbx/model/model.py", line 478, in get_xray_structure assert cs is not None AssertionError

Thanks in advance for your help again. I hope I'm not kicking too much of a can of worms here.

Best wishes,

-- Ricardo Diogo Righetto

Em qua., 2 de abr. de 2025 às 21:12, Alexandre OURJOUMTSEV escreveu:

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-- Tim Gruene Head of the CF Crystal Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A