## [Jmol-users] puttting the protein molecule in a grid and navigating it with a cube of user-defined radius

 [Jmol-users] puttting the protein molecule in a grid and navigating it with a cube of user-defined radius From: Anasuya Dighe - 2011-12-29 07:39:10 ```Hello, How do i put an entire protein molecule inside a cube/grid with x-axis spanning till the largest x-coordinate, y-axis spanning till the largest y-coordinate, and z-axis spanning till the largest z-coordinate? Once i do this, can i divide the larger cube(i.e. the one holding the entire protein) into smaller ones of lesser dimensions? Say, 2A x 2A x 2A? Once i generate these smaller cubes, is there a way via Jmol, by which i can navigate through the protein molecule, (smaller)cube by (smaller)cube? As in, can Jmol be used to tell me which residues are lying in which (smaller) cube and so on? I am aware that it is possible to integrate objects like spheres and grids into Jmol, but i dont know how to address the following problem and visualise the same? Please let me know. Thanks, - Anasuya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ```

 [Jmol-users] puttting the protein molecule in a grid and navigating it with a cube of user-defined radius From: Anasuya Dighe - 2011-12-29 07:39:10 ```Hello, How do i put an entire protein molecule inside a cube/grid with x-axis spanning till the largest x-coordinate, y-axis spanning till the largest y-coordinate, and z-axis spanning till the largest z-coordinate? Once i do this, can i divide the larger cube(i.e. the one holding the entire protein) into smaller ones of lesser dimensions? Say, 2A x 2A x 2A? Once i generate these smaller cubes, is there a way via Jmol, by which i can navigate through the protein molecule, (smaller)cube by (smaller)cube? As in, can Jmol be used to tell me which residues are lying in which (smaller) cube and so on? I am aware that it is possible to integrate objects like spheres and grids into Jmol, but i dont know how to address the following problem and visualise the same? Please let me know. Thanks, - Anasuya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ```
 Re: [Jmol-users] puttting the protein molecule in a grid and navigating it with a cube of user-defined radius From: Robert Hanson - 2011-12-30 18:31:33 Attachments: Message as HTML ```The boundbox object can do this. You can set it to whatever size you want and place it wherever you want, and then you can use select within(boundbox) On Thu, Dec 29, 2011 at 1:16 AM, Anasuya Dighe wrote: > Hello, > > How do i put an entire protein molecule inside a cube/grid with x-axis > spanning > till the > largest x-coordinate, y-axis spanning till the largest y-coordinate, and > z-axis > spanning till the largest z-coordinate? > > Once i do this, can i divide the larger cube(i.e. the one holding the > entire > protein) into smaller ones of lesser dimensions? Say, 2A x 2A x 2A? > > Once i generate these smaller cubes, is there a way via Jmol, by which i > can > navigate through the protein molecule, (smaller)cube by (smaller)cube? > As in, can Jmol be used to tell me which residues are lying in which > (smaller) > cube and so on? > > I am aware that it is possible to integrate objects like spheres and grids > into > Jmol, but i dont know how to address the following problem and visualise > the > same? > > Please let me know. > Thanks, > - Anasuya > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > > > ------------------------------------------------------------------------------ > Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex > infrastructure or vast IT resources to deliver seamless, secure access to > virtual desktops. With this all-in-one solution, easily deploy virtual > desktops for less than the cost of PCs and save 60% on VDI infrastructure > costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ```