## Re: [PyMOL] Help/suggestions for illustrating lattice arrangement

 Re: [PyMOL] Help/suggestions for illustrating lattice arrangement From: Robert Campbell - 2004-10-07 19:04:01 ```Hi Roger, * Roger Dodd [2004-10-07 16:33] wrote: >=20 > I am trying to prepare a figure illustrating a fairly complex packing=20 > arrangement in a large H32 (R32) unit cell, where the packing may=20 > actually have some biological relevance. To try and show the packing=20 > I've been generating symmetry related molecules using the symexp=20 > command. The problem I've been running into is that things become too=20 > complex and cluttered, whether I use lines, ribbons, cartoons, etc. My=20 > asymmetric unit contains 2 homo-pentamers and my question is - would it= =20 > be possible to replace each monomer with, for example, an ellipsoid of=20 > roughly the same size centred on the subunit's centre of mass to=20 > simplify things? Is this the sort of thing that could be done with a cgo= =20 > object? Any help or other suggestions would be greatly appreciated. You could set solvent_radius to some large number, like 5 or 10 and show the molecules' surface. The main problem is that there tend to be holes in the surface unless you set the surface_quality up to 1, in which case it can take quite a bit longer to draw. A CGO ellipsoid might be your best bet, but I'm not sure if there is a CGO ellipsoid. An approximation to the ellipsoid could be the "SAUSAGE" instead: =66rom pymol.cgo import * =66rom pymol import cmd # simple example obj2 =3D [ SAUSAGE, 0., 0., 0., 10., 0., 0., 4.0, 1.0, 1.0, 1.0, 0.5, 0.0, 0., SAUSAGE, 0., 0., 0., 0., 15., 0., 4.0, 1.0, 1.0, 1.0, 0., 0.5, 0., SAUSAGE, 0., 0., 0., 0., 0., 20., 4.0, 1.0, 1.0, 1.0, 0., 0.0, 0.5, ] cmd.load_cgo(obj2,'cyl') You would need to come up with appropriate starting and ending vertices (the first 6 numbers in each line) and the radius (the 7th number). The last 6 numbers are the starting and ending rgb colour values. I guess whether this could work would depend on how close your monomer could be approximated by a sausage. :) Cheers, Rob --=20 Robert L. Campbell, Ph.D. Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 ```

 [PyMOL] Help/suggestions for illustrating lattice arrangement From: Roger Dodd - 2004-10-07 15:33:43 ```Hi, I am trying to prepare a figure illustrating a fairly complex packing arrangement in a large H32 (R32) unit cell, where the packing may actually have some biological relevance. To try and show the packing I've been generating symmetry related molecules using the symexp command. The problem I've been running into is that things become too complex and cluttered, whether I use lines, ribbons, cartoons, etc. My asymmetric unit contains 2 homo-pentamers and my question is - would it be possible to replace each monomer with, for example, an ellipsoid of roughly the same size centred on the subunit's centre of mass to simplify things? Is this the sort of thing that could be done with a cgo object? Any help or other suggestions would be greatly appreciated. Cheers Roger ```
 Re: [PyMOL] Help/suggestions for illustrating lattice arrangement From: Robert Campbell - 2004-10-07 19:04:01 ```Hi Roger, * Roger Dodd [2004-10-07 16:33] wrote: >=20 > I am trying to prepare a figure illustrating a fairly complex packing=20 > arrangement in a large H32 (R32) unit cell, where the packing may=20 > actually have some biological relevance. To try and show the packing=20 > I've been generating symmetry related molecules using the symexp=20 > command. The problem I've been running into is that things become too=20 > complex and cluttered, whether I use lines, ribbons, cartoons, etc. My=20 > asymmetric unit contains 2 homo-pentamers and my question is - would it= =20 > be possible to replace each monomer with, for example, an ellipsoid of=20 > roughly the same size centred on the subunit's centre of mass to=20 > simplify things? Is this the sort of thing that could be done with a cgo= =20 > object? Any help or other suggestions would be greatly appreciated. You could set solvent_radius to some large number, like 5 or 10 and show the molecules' surface. The main problem is that there tend to be holes in the surface unless you set the surface_quality up to 1, in which case it can take quite a bit longer to draw. A CGO ellipsoid might be your best bet, but I'm not sure if there is a CGO ellipsoid. An approximation to the ellipsoid could be the "SAUSAGE" instead: =66rom pymol.cgo import * =66rom pymol import cmd # simple example obj2 =3D [ SAUSAGE, 0., 0., 0., 10., 0., 0., 4.0, 1.0, 1.0, 1.0, 0.5, 0.0, 0., SAUSAGE, 0., 0., 0., 0., 15., 0., 4.0, 1.0, 1.0, 1.0, 0., 0.5, 0., SAUSAGE, 0., 0., 0., 0., 0., 20., 4.0, 1.0, 1.0, 1.0, 0., 0.0, 0.5, ] cmd.load_cgo(obj2,'cyl') You would need to come up with appropriate starting and ending vertices (the first 6 numbers in each line) and the radius (the 7th number). The last 6 numbers are the starting and ending rgb colour values. I guess whether this could work would depend on how close your monomer could be approximated by a sausage. :) Cheers, Rob --=20 Robert L. Campbell, Ph.D. Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 ```
 Re: [PyMOL] Help/suggestions for illustrating lattice arrangement From: Tsjerk Wassenaar - 2004-10-08 10:21:35 ```Hi Roger, Unfortunately, there is no CGO ellipsoid. What you might try is represent the units in the lattice as arrows as to indicate their orientation (determined as the principal or principle ;) axis), and have one unit in (cartoon) detail, with a more slender arrow inside. I think it would give enough idea to the viewer of how the thing is packed :) Hope it helps, Tsjerk You can create an arrow by using a cylinder and a set of ever smaller spheres for the arrow tip. Robert Campbell wrote: >Hi Roger, > >* Roger Dodd [2004-10-07 16:33] wrote: > > >>I am trying to prepare a figure illustrating a fairly complex packing >>arrangement in a large H32 (R32) unit cell, where the packing may >>actually have some biological relevance. To try and show the packing >>I've been generating symmetry related molecules using the symexp >>command. The problem I've been running into is that things become too >>complex and cluttered, whether I use lines, ribbons, cartoons, etc. My >>asymmetric unit contains 2 homo-pentamers and my question is - would it >>be possible to replace each monomer with, for example, an ellipsoid of >>roughly the same size centred on the subunit's centre of mass to >>simplify things? Is this the sort of thing that could be done with a cgo >>object? Any help or other suggestions would be greatly appreciated. >> >> > >You could set solvent_radius to some large number, like 5 or 10 >and show the molecules' surface. The main problem is that there tend >to be holes in the surface unless you set the surface_quality up to 1, >in which case it can take quite a bit longer to draw. A CGO ellipsoid >might be your best bet, but I'm not sure if there is a CGO ellipsoid. > >An approximation to the ellipsoid could be the "SAUSAGE" instead: > >from pymol.cgo import * >from pymol import cmd > ># simple example > >obj2 = [ > SAUSAGE, 0., 0., 0., 10., 0., 0., 4.0, 1.0, 1.0, 1.0, 0.5, 0.0, 0., > SAUSAGE, 0., 0., 0., 0., 15., 0., 4.0, 1.0, 1.0, 1.0, 0., 0.5, 0., > SAUSAGE, 0., 0., 0., 0., 0., 20., 4.0, 1.0, 1.0, 1.0, 0., 0.0, 0.5, > ] >cmd.load_cgo(obj2,'cyl') > >You would need to come up with appropriate starting and ending vertices >(the first 6 numbers in each line) and the radius (the 7th number). The >last 6 numbers are the starting and ending rgb colour values. > >I guess whether this could work would depend on how close your monomer >could be approximated by a sausage. :) > >Cheers, >Rob > > -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- :) -- :) Tsjerk A. Wassenaar, M.Sc. -- :) Molecular Dynamics Group -- :) Dept. of Biophysical Chemistry -- :) University of Groningen -- :) Nijenborgh 4 -- :) 9747 AG Groningen -- :) The Netherlands -- :) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- :) -- :) Hi! I'm a .signature virus! -- :) Copy me into your ~/.signature to help me spread! -- :) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ```
 Re: [PyMOL] Help/suggestions for illustrating lattice arrangement From: Peter Haebel - 2004-10-08 12:27:33 ```Hi Roger, the easiest solution is probably to create a fake pdb file with dummy atoms= =20 (located roughly in the center of mass) to represent each molecule in your= =20 ASU. make sure the pdb file contains the same CRYST entry as your original file. you can load it into pymol and then scale up the atom radius to approximate= =20 the size of your molecule. set sphere_scale, 5.0 show spheres, all and finally create the symmetry related 'molecules' with symexp. cheers, peter =20 On Thursday 07 October 2004 17:33, Roger Dodd wrote: > Hi, > > I am trying to prepare a figure illustrating a fairly complex packing > arrangement in a large H32 (R32) unit cell, where the packing may > actually have some biological relevance. To try and show the packing > I've been generating symmetry related molecules using the symexp > command. The problem I've been running into is that things become too > complex and cluttered, whether I use lines, ribbons, cartoons, etc. My > asymmetric unit contains 2 homo-pentamers and my question is - would it > be possible to replace each monomer with, for example, an ellipsoid of > roughly the same size centred on the subunit's centre of mass to > simplify things? Is this the sort of thing that could be done with a cgo > object? Any help or other suggestions would be greatly appreciated. > > Cheers > > Roger > > > ------------------------------------------------------- > This SF.net email is sponsored by: IT Product Guide on ITManagersJournal > Use IT products in your business? Tell us what you think of them. Give us > Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out mo= re > http://productguide.itmanagersjournal.com/guidepromo.tmpl > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@... > https://lists.sourceforge.net/lists/listinfo/pymol-users =2D-=20 ___________________________________________ Dr. Peter Haebel Philipps-Universit=E4t Marburg Institut f=FCr Pharmazeutische Chemie Marbacher Weg 6 D-35032 Marburg phone: +49-6421-28-25072 fax: +49-6421-28-28994 email: peter.haebel@... http://www.agklebe.de ```