Fwd: chimera to rebuild crystal
Hi Tom, Brady's question below seems more up your alley somehow. It also seems like one of those things that should be cross-posted to the chimera-users or -dev lists for "community building" purposes, though I'll leave that up to your discretion. --Eric Begin forwarded message:
From: "Brady Bernard" <bradyb@u.washington.edu> Date: January 11, 2007 5:06:21 PM PST To: "Eric Pettersen" <pett@cgl.ucsf.edu> Subject: chimera to rebuild crystal
hi, i am interested in using distance-dependent statistics in a scoring function and i would like more than the default 3x3x3 repeating units to rebuild a crystal using cryst1 data in pdb files. how can i do this with chimera? i will need to do this for thousands of files and am familiar with scripting and using the -nogui option with cmd files, etc. thanks in advance for your help, brady bernard uw bioengineering
Hi Brady, When you say "rebuild a crystal" do you mean you want to open many copies of the asymmetric unit to form a 5x5x5 (for example) block of unit cells? Or do you mean you want the Chimera "multiscale model" where just one copy of the asym unit is opened but surfaces can be shown for the others? Both are possible using Chimera scripts. What sort of "distance-dependent statistics" are you talking about? Are they going to be calculated within Chimera? or is Chimera just used for displaying some result? Perhaps I missed some previous email to Eric Pettersen that would help me understand what you need. Tom
hi tom ... multiscale modeling would be too restrictive - your 5x5x5 example (or any other number that i can modify in a chimera script) is more adequate. i would like to make the n x n x n structure, save it to a PDB, and use perl or some other program separately to process the pdb file and perform the statistics. so chimera would take the single molecule with cryst1 data, make the larger crystal, and write it out to a pdb. hope that helps - let me know if you have any other questions. thanks, brady ----- Original Message ----- From: "Thomas Goddard" <goddard@cgl.ucsf.edu> To: <bradyb@u.washington.edu> Cc: <pett@cgl.ucsf.edu>; <goddard@cgl.ucsf.edu> Sent: Thursday, January 11, 2007 7:48 PM Subject: Re: Fwd: chimera to rebuild crystal
Hi Brady,
When you say "rebuild a crystal" do you mean you want to open many copies of the asymmetric unit to form a 5x5x5 (for example) block of unit cells? Or do you mean you want the Chimera "multiscale model" where just one copy of the asym unit is opened but surfaces can be shown for the others? Both are possible using Chimera scripts.
What sort of "distance-dependent statistics" are you talking about? Are they going to be calculated within Chimera? or is Chimera just used for displaying some result? Perhaps I missed some previous email to Eric Pettersen that would help me understand what you need.
Tom
Hi Brady, Ok, that helps. Might be easiest to not open all those copies of the PDB asym unit in Chimera but instead open one and then use Chimera routines to output many transformed copies. Would you want all the copies in a single PDB file? That presents the problem that you'll have many copies with the same chain ID's and residue numbers and how will you know which unit cell and symmetry each atom belongs to. Maybe that isn't needed for your statistics? Do the statistics involve interface interactions? Also you may exceed the PDB format 100,000 atom limit (serial number can only be 5 digits) if they all go in one file. The different copies could be written to separate files with names based on which unit cell and symmetry operator was used. If I know exactly what you need I might be able to send a script your way tomorrow. Tom
hi tom ...
The different copies could be written to separate files with names based on which unit cell and symmetry operator was used.
i think that sounds like a good solution. thanks, brady ----- Original Message ----- From: "Thomas Goddard" <goddard@cgl.ucsf.edu> To: <bradyb@u.washington.edu> Cc: <goddard@cgl.ucsf.edu> Sent: Thursday, January 11, 2007 8:06 PM Subject: Re: Fwd: chimera to rebuild crystal
Hi Brady,
Ok, that helps. Might be easiest to not open all those copies of the PDB asym unit in Chimera but instead open one and then use Chimera routines to output many transformed copies. Would you want all the copies in a single PDB file? That presents the problem that you'll have many copies with the same chain ID's and residue numbers and how will you know which unit cell and symmetry each atom belongs to. Maybe that isn't needed for your statistics? Do the statistics involve interface interactions? Also you may exceed the PDB format 100,000 atom limit (serial number can only be 5 digits) if they all go in one file. The different copies could be written to separate files with names based on which unit cell and symmetry operator was used.
If I know exactly what you need I might be able to send a script your way tomorrow.
Tom
Hi Brady, I wrote a Python script that writes copies of a PDB model transformed to fill out a block of unit cells. You can get it from the Chimera experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html See the "details" link on that page for info about the script. Tom
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Tom, Something that would be really good for crystallographers ( or at the very least for this crystallographer ;-) ) is a way of getting the symmetry related molecules that are in a certain radius of a selection. As far as I know that is not possible now. I can get a full unit cell and, if I recall it correctly, maybe a translated unit cell. While this would in the end produce the symmetry related molecules around a particular selection, being able to do it with a single command and showing just those within that radius would be very helpful. It's not an urgent need, just for your "wish-list" if it's not too full! Big thanks to all the team for Chimera! And happy new year to everyone! Miguel En/na Thomas Goddard ha escrit:
Hi Brady,
I wrote a Python script that writes copies of a PDB model transformed to fill out a block of unit cells. You can get it from the Chimera experimental features web page:
http://www.cgl.ucsf.edu/chimera/experimental/experimental.html
See the "details" link on that page for info about the script.
Tom _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
- -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork@yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFFp/eRF6oOrDvhbQIRAkapAJkBVCfmewkE6F0vmnbj05m3hKZPBgCfR8ak C7XmyntMOa+u99In5WWNUwI= =6GQg -----END PGP SIGNATURE-----
Hi Miguel, Yeah, I have had on my to-do list to allow creating all asymmetric units that contact a given unit (atom to atom distance less than a specified value). Using just a radius (measured from centers of bounding boxes would be simpler. I've added that to my to-do list. Also I want to add the ability to interactively move all the surrounding subunits radially to allow easy inspection of the interfaces, kind of like the Mac expose feature for moving windows so they don't overlap. It would be quickly reversible and maybe good for animations. Thanks, Tom
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Tom, That would be truly fantastic! Not only for animations, it would help a lot to inspect and compare crystal contacts. Thanks to you! Eager to see the result ;-) Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork@yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFFp/vBF6oOrDvhbQIRAlIBAJ9m3/KyYyV9TDlX735AaEM2N1hW4ACfURuA k7Bszy56Ut7N1PoJzeRo2ls= =fFIt -----END PGP SIGNATURE-----
Hi Tom, Can't a person just use Unit Cell and then Write PDB (i.e. is this a shortcut provided as a convenience, or different somehow)? Thanks Elaine On Jan 12, 2007, at 12:26 PM, Thomas Goddard wrote:
Hi Brady,
I wrote a Python script that writes copies of a PDB model transformed to fill out a block of unit cells. You can get it from the Chimera experimental features web page:
http://www.cgl.ucsf.edu/chimera/experimental/experimental.html
See the "details" link on that page for info about the script.
Tom _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
thank you very much. you guys rock! i've have tried it out preliminarily and it looks great. i'll be in touch if i have any more questions or requests. brady ----- Original Message ----- From: "Thomas Goddard" <goddard@cgl.ucsf.edu> To: <bradyb@u.washington.edu> Cc: <chimera-users@cgl.ucsf.edu> Sent: Friday, January 12, 2007 12:26 PM Subject: chimera to rebuild crystal
Hi Brady,
I wrote a Python script that writes copies of a PDB model transformed to fill out a block of unit cells. You can get it from the Chimera experimental features web page:
http://www.cgl.ucsf.edu/chimera/experimental/experimental.html
See the "details" link on that page for info about the script.
Tom
hi tom - is there a quick way to save the atom types from idatmType to a text/log file along with the atom name or number? thanks, brady ----- Original Message ----- From: "Thomas Goddard" <goddard@cgl.ucsf.edu> To: <bradyb@u.washington.edu> Cc: <chimera-users@cgl.ucsf.edu> Sent: Friday, January 12, 2007 12:26 PM Subject: chimera to rebuild crystal
Hi Brady,
I wrote a Python script that writes copies of a PDB model transformed to fill out a block of unit cells. You can get it from the Chimera experimental features web page:
http://www.cgl.ucsf.edu/chimera/experimental/experimental.html
See the "details" link on that page for info about the script.
Tom
participants (5)
-
Brady Bernard -
Elaine Meng -
Eric Pettersen -
Miguel Ortiz-Lombardia -
Thomas Goddard