Hello,
Today I was trying to display a crystal packing from a PDB entry in ChimeraX, but could not find how to do this. I read the documentation for the sym command https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html ; but either I didn’t get it, or this is not the adequate command for what I am trying to do.
What I want to do is the equivalent of PyMOL’s "Action / generate / symmetry mates / +/- one unit cell and within… Å", which is different from the biological assembly the sym command can generate from the PDB annotation. When working with crystallographic data, ISOLDE displays molecules related to the working model by crystallographic symmetry, so displaying the crystal packing seems doable in ChimeraX. Or is it one of ISOLDE’s additions?
It would be wonderful if someone could help me with this (it is one of the last few things I need on a regular basis, that I still don’t know how to do in ChimeraX).
Thank you in advance,
Guillaume
The symmetry display in ISOLDE is actually provided by the Clipper plugin (which I’m also responsible for). It doesn’t currently have a built-in command to turn the symmetry views into real atoms, but it wouldn’t be particularly difficult to add that. Is actual copies of the molecules what you want? Or are instanced “ghost” copies of the main molecule sufficient?
On 8 May 2020, at 14:24, Guillaume Gaullier guillaume@gaullier.org wrote:
Hello,
Today I was trying to display a crystal packing from a PDB entry in ChimeraX, but could not find how to do this. I read the documentation for the sym command https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html ; but either I didn’t get it, or this is not the adequate command for what I am trying to do.
What I want to do is the equivalent of PyMOL’s "Action / generate / symmetry mates / +/- one unit cell and within… Å", which is different from the biological assembly the sym command can generate from the PDB annotation. When working with crystallographic data, ISOLDE displays molecules related to the working model by crystallographic symmetry, so displaying the crystal packing seems doable in ChimeraX. Or is it one of ISOLDE’s additions?
It would be wonderful if someone could help me with this (it is one of the last few things I need on a regular basis, that I still don’t know how to do in ChimeraX).
Thank you in advance,
Guillaume
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
I need to measure distances between the main model’s atoms and atoms in the symmetry copies, and I also need to be able to tweak the representation (cartoon, sticks, colors, etc.) in any way ChimeraX will allow independently between the main model and the symmetry copies.
Guillaume
On 8 May 2020, at 15:54, Tristan Croll tic20@CAM.AC.UK wrote:
The symmetry display in ISOLDE is actually provided by the Clipper plugin (which I’m also responsible for). It doesn’t currently have a built-in command to turn the symmetry views into real atoms, but it wouldn’t be particularly difficult to add that. Is actual copies of the molecules what you want? Or are instanced “ghost” copies of the main molecule sufficient?
On 8 May 2020, at 14:24, Guillaume Gaullier guillaume@gaullier.org wrote:
Hello,
Today I was trying to display a crystal packing from a PDB entry in ChimeraX, but could not find how to do this. I read the documentation for the sym command https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html ; but either I didn’t get it, or this is not the adequate command for what I am trying to do.
What I want to do is the equivalent of PyMOL’s "Action / generate / symmetry mates / +/- one unit cell and within… Å", which is different from the biological assembly the sym command can generate from the PDB annotation. When working with crystallographic data, ISOLDE displays molecules related to the working model by crystallographic symmetry, so displaying the crystal packing seems doable in ChimeraX. Or is it one of ISOLDE’s additions?
It would be wonderful if someone could help me with this (it is one of the last few things I need on a regular basis, that I still don’t know how to do in ChimeraX).
Thank you in advance,
Guillaume
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
This should do what you want (you'll need Clipper installed - also ISOLDE if you choose to use the commented-out alternative option at the bottom). Just copy the below script into a file called make_unit_cells.py, open and select your model, then do:
run make_unit_cells.py num_u, num_v, num_w
... where num_u, num_v and num_w are the number of unit cells to pad by along each dimension (i.e. 0 0 0 will give you a single unit cell, 1 1 1 will give you 3x3x3). Values greater than 1 are probably inadvisable.
I've put two options at the end of the script. The first (the one it's currently set to use) uses the methods from ChimeraX's sym command, which creates each copy as a separate model, in the new position but otherwise identical (same chain ID). The other, commented-out option uses an alternative from ISOLDE which will merge them into the *same* model with new chain IDs - but be aware that this is not yet optimised for performance (the time required blows out geometrically with the number of copies - a couple of dozen is fine, but an attempt to make a 3x3x3 unit cells from a 300-residue model with 27 copies in the unit cell - i.e. 729 ASUs - is at half an hour and counting). If you want to use it, just comment these lines:
from chimerax.std_commands import sym sym.show_symmetry([m], 'unit cells', Places(places), True, False, False, None, None, m.session)
... and uncomment these ones:
# from chimerax.isolde.atomic.building.ncs import create_all_ncs_copies # create_all_ncs_copies(m, places)
# Script starts here
import sys import numpy
args = sys.argv if len(args) != 4: from chimerax.core.errors import UserError raise UserError('Arguments should be the number of unit cells to pad by along each axis!') padding = numpy.array([int(r) for r in args[1:]])
from chimerax.atomic import selected_atoms m = selected_atoms(session).unique_structures[0]
def expand_to_unit_cells(m, padding): min_bound = -padding max_bound = padding
from chimerax.clipper.symmetry import ( symmetry_from_model_metadata, Unit_Cell )
from chimerax.clipper import RTop_frac
cell, spacegroup, sampling, res, _ = symmetry_from_model_metadata(m) uc = Unit_Cell(m.atoms, cell, spacegroup, sampling)
from chimerax.geometry import Places, Place uc_symops = uc.symops
from chimerax.geometry import Place, Places places = [] from chimerax.clipper import Coord_frac for du in range(min_bound[0], max_bound[0]+1): for dv in range(min_bound[1], max_bound[1]+1): for dw in range(min_bound[2], max_bound[2]+1): for s in uc_symops: this_s = RTop_frac(s.rot, s.trn+Coord_frac(du,dv,dw)) ts_orth = this_s.rtop_orth(cell) places.append(Place(axes=ts_orth.rot.as_numpy().T, origin=ts_orth.trn.as_numpy()))
print('Number of transforms: {}'.format(len(places)))
# This option is fast, but places each copy into a separate model with the # same chain ID as the original from chimerax.std_commands import sym sym.show_symmetry([m], 'unit cells', Places(places), True, False, False, None, None, m.session)
# This method will merge the new chains into the current model with new # chain IDs, but currently gets *incredibly* slow if there are large numbers # of copies involved.
# from chimerax.isolde.atomic.building.ncs import create_all_ncs_copies # create_all_ncs_copies(m, places)
expand_to_unit_cells(m, padding)
On 2020-05-08 14:54, Tristan Croll wrote:
The symmetry display in ISOLDE is actually provided by the Clipper plugin (which I’m also responsible for). It doesn’t currently have a built-in command to turn the symmetry views into real atoms, but it wouldn’t be particularly difficult to add that. Is actual copies of the molecules what you want? Or are instanced “ghost” copies of the main molecule sufficient?
On 8 May 2020, at 14:24, Guillaume Gaullier guillaume@gaullier.org wrote:
Hello,
Today I was trying to display a crystal packing from a PDB entry in ChimeraX, but could not find how to do this. I read the documentation for the sym command https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html ; but either I didn’t get it, or this is not the adequate command for what I am trying to do.
What I want to do is the equivalent of PyMOL’s "Action / generate / symmetry mates / +/- one unit cell and within… Å", which is different from the biological assembly the sym command can generate from the PDB annotation. When working with crystallographic data, ISOLDE displays molecules related to the working model by crystallographic symmetry, so displaying the crystal packing seems doable in ChimeraX. Or is it one of ISOLDE’s additions?
It would be wonderful if someone could help me with this (it is one of the last few things I need on a regular basis, that I still don’t know how to do in ChimeraX).
Thank you in advance,
Guillaume
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Guillaume,
Showing contacting asymmetric units in crystal hasn't been added to ChimeraX, but I will add it. What you want is the crystalcontacts command from Chimera.
https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/crystalcontac...
Chimera has 25 years of accumulated features and we are moving all the good stuff to ChimeraX but it takes time. During the transition I advise using both programs for what they do best. I would make the crystal contacts in Chimera, write a PDB, and open it in ChimeraX. Here's an example.
In Chimera,
open 1a0m crystalcontacts #0 10 copies true schematic false menu File / Save PDB..., save all in a single PDB file 1a0m_range10.pdb
In ChimeraX
open 1a0m_range10.pdb show surface
Tom
On May 8, 2020, at 6:24 AM, Guillaume Gaullier guillaume@gaullier.org wrote:
Hello,
Today I was trying to display a crystal packing from a PDB entry in ChimeraX, but could not find how to do this. I read the documentation for the sym command https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html ; but either I didn’t get it, or this is not the adequate command for what I am trying to do.
What I want to do is the equivalent of PyMOL’s "Action / generate / symmetry mates / +/- one unit cell and within… Å", which is different from the biological assembly the sym command can generate from the PDB annotation. When working with crystallographic data, ISOLDE displays molecules related to the working model by crystallographic symmetry, so displaying the crystal packing seems doable in ChimeraX. Or is it one of ISOLDE’s additions?
It would be wonderful if someone could help me with this (it is one of the last few things I need on a regular basis, that I still don’t know how to do in ChimeraX).
Thank you in advance,
Guillaume
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Guillaume Gaullier -
Tom Goddard -
Tristan Croll