[cctbxbb] Generating crystal copies

[Oleg Sobolev]

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, <markus.gerstel at diamond.ac.uk> 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:* cctbxbb-bounces at phenix-online.org [mailto:
> cctbxbb-bounces at phenix-online.org] *On Behalf Of *Nicholas Pearce
> *Sent:* 07 April 2015 17:26
> *To:* cctbxbb at phenix-online.org
> *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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