Hi, in addition, see implementation of iotbx.show_distances your.pdb > all_distances that will output potentially long file with distances "all with all" (with some cut-off I think) including symmetry related. Also, a method expand_to_p1() of xray.structure (cctbx/xray/structure.py) may be of help: this will expand model into P1 (isn't it what you want!). Actual code that does the calculations: cctbx_project/cctbx/xray/scatterer_utils.h (expand_to_p1) All in all, cctbx offers a variety of tools to do what you want. Perhaps someone needs to add a command like iotbx.expand_to_p1 your_model_in_any_space_group.pdb > model_p1.pdb though it sounds like you want this at your script level, not as end-user-ready application. Let me know if you have more questions or need help with this. Pavel On 4/7/15 2:16 PM, Oleg Sobolev wrote:

Hi Nicholas,

Please find the script for searching contacts attached. It reads in .pdb file (file name is passed through command-line arg) and prints out symmetry contacts with some additional info. Hopefully this will help, or feel free to ask more questions. I believe that you have already read this description of the machinery you are trying to use:

http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf

Best regards, Oleg Sobolev.

On Tue, Apr 7, 2015 at 9:33 AM, mailto:[email protected]> wrote:

Dear Nicholas,

I found the CCP4 program ncont to be the easiest way to identify crystal contacts.

If you’re interested in a completed unit cell I have a PDBCUR/PDBSET script somewhere, which might provide a useful starting point.

I have tried using cctbx a couple of years back to compute either of these, but got inconsistent results. (Also at that time I didn’t really know what I’m doing. Which may still be true.)

-Markus

*From:*[email protected] mailto:[email protected] [mailto:[email protected] mailto:[email protected]] *On Behalf Of *Nicholas Pearce *Sent:* 07 April 2015 17:26 *To:* [email protected] mailto:[email protected] *Subject:* [cctbxbb] Generating crystal copies

Hi Everyone,

I'm currently trying to generate crystal contacts/copies. What I want out at the end is a list of symmetry operations to generate the crystallographic copies that form contacts with my input model.

I've been using the asu_mappings object, but I'm not sure I'm using the output correctly or if it's the right thing to use.

Code snippet used to calculate the mappings:

# Extract the xray structure from the reference hierarchy ref_struc = ref_hierarchy.extract_xray_structure(crystal_symmetry=crystal_symmetry)

# Extract the mappings that will tell us the adjacent symmetry copies asu_mappings = ref_struc.asu_mappings(buffer_thickness=5)

# Symmetry operations for each atom mappings = asu_mappings.mappings()

I printed out all of the mappings, as I presumed the vast majority of the them would be the identity, meaning that any non-identity operations would be from atoms in the buffer area I have defined. These non-identity operations would presumably be the ones that would generate the crystal contacts.

However, a large number of the atoms only had one mapping, which was not the identity - e.g. asu_mappings.get_rt_mx(x).as_xyz() might give '-x+1/2,-y+1/2,z-1/2' for an atom with only one mapping.

The effect of this is that the operations given by this generate symmetry copies that do not contact my input model in real space.

I presume this means that asu_mappings is mapping the atoms in my model to some other arbitrary asu, as well as the atoms in the buffer zone around it? Therefore the symmetry operations given are for these mapped atoms?

Can anyone help, or suggest an alternative way to generate the crystal contacts?

Thanks, Nick

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