- cctbxbb - phenix-online.org

reduce2 and cell construction from python script
by Enrico Ravera 14 Feb '25

14 Feb '25

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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getting indices of selected grid elements of a map
by robert＠oeffner.net 20 Jan '25

20 Jan '25

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

2 4

atomic density profile at finite resolution
by robert＠oeffner.net 12 Dec '24

12 Dec '24

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

4 8

cluster coordinates to asymmetric unit
by robert＠oeffner.net 05 Dec '24

05 Dec '24

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

3 2

chiral validation
by James Holton 04 Nov '24

04 Nov '24

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

2 1

electron density value near an atom
by robert＠oeffner.net 14 Oct '24

14 Oct '24

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

3 2

Hardware migration
by Billy Poon 19 Jun '24

19 Jun '24

Hi everyone, We are in the process of migrating these bulletin boards to new hardware over the next few weeks. I will make another post once the migration is completed. Nothing will be changed until then. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

1 2

Test thread from website
by bkpoon＠lbl.gov 19 Jun '24

19 Jun '24

The bulletin board update has also enabled posting from the website

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test post
by bkpoon＠lbl.gov 16 Jun '24

16 Jun '24

This is a test message

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test post
by bkpoon＠lbl.gov 16 Jun '24

16 Jun '24

This is a test message

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