May 2026 - cctbxbb - phenix-online.org

electron density value near an atom
by robert＠oeffner.net 06 Jun '26

06 Jun '26

Dear CCTBX users/developers I would like to calculate the theoretical electron density value at a point in space as a function of an atom specified by its coordinate and its form factor. I’ll assume it’s for a certain X-ray wavelength, say 1.0Å. If someone would have the time to give me a few pointers on how to do this using the CCTBX I'd be very grateful. Thanks in advance, Rob

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chiral validation
by James Holton 06 Jun '26

06 Jun '26

Can anyone tell me the units of the numbers being displayed by phenix.chiral_validation? The --help documentation doesn't mention anything about chirality. Seems to be a copy of the documentation for omegalyze? Just thought that might be of interest, and I also want to know what the numbers mean. Cheers, -James

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cluster coordinates to asymmetric unit
by robert＠oeffner.net 06 Jun '26

06 Jun '26

Hi, I'm trying to work out how to cluster atomic coordinates into one asymmetric unit in a crystal for a given spacegroup rather than the atomic coordinates placed in arbitrary asymmetric unit copies in the unit cell. I think the tools to be used must be in cctbx.crystal.direct_space_asu and I have been trying but failed to understand how the test tst_crystal_asu_clusters.py works. Is there already a phenix or cctbx program that can do this? Many thanks, Robert

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atomic density profile at finite resolution
by robert＠oeffner.net 06 Jun '26

06 Jun '26

I came across this article https://doi.org/10.1107/S160057672201144X. Although I have yet to read it in details I wonder if the CCTBX can Fcalc maps at finite resolution, i.e. not using Gaussian atomic density profiles. It looks like the function in cctbx.maptbx.atom_curves.bcr_approx(...) is suited to do so. If so, how would I use this for generating a real space map as in https://cci.lbl.gov/docs/cctbx/script_1/#create-a-map-from-a-pdb-file but now using atomic density profiles at finite resolution? Many thanks, Robert

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getting indices of selected grid elements of a map
by robert＠oeffner.net 06 Jun '26

06 Jun '26

Hi, I am wondering if there is an efficient way to retrieve the 3D indices of a selection from a map. In the example on https://cci.lbl.gov/docs/cctbx/doc_low_flex_advanced/#getting-indices-of-se… it is shown how to list the indices of a subset of grid elements of the map as in print(list(isel)) But isel is a 1D representation of 3d map indices. What if I want to get hold of the list of 3D indices corresponding to the indices in the isel array? Is there a fast boost-python way of doing this or would I have to do a 3D loop over the unit cell grid numbers to see if enumerated grid elements matches any of the elements in the isel array? Many thanks, Rob

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reduce2 and cell construction from python script
by Enrico Ravera 06 Jun '26

06 Jun '26

Hi, I apologize for the naive post. I am trying to figure out how to perform the following tasks: 1) read in a mmcif file (which I think I can do following the tutorial); 2) trim the solvent and hydrogen atoms (probably I can do it following the tutorial); 3) run reduce2 to get hydrogens in the nuclear positions (no clue); 4) get the full content of the unit cell (no clue). Any help is appreciated. All the best, Enrico

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