phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups
PHENIX users: starting dev-610 (development version of PHENIX) there is a new tool available for completely automated partitioning a model into TLS groups: http://www.phenix-online.org/download/nightly_builds.cgi To run: phenix.find_tls_groups model.pdb or if you have a multiple CPU machine: phenix.find_tls_groups model.pdb nproc=N where N is the number of CPUs available (thanks Nat for parallelization!). There is no parameters that a user is supposed to tweak (except defining the number of CPUs, if desired). The result of running the above command are atom selections that define TLS groups. These atom selections are ready to use in phenix.refine. This is available from PHENIX GUI too, where automatically defined TLS groups can be readily visualized and checked on the graphics (thanks Nat!). The algorithm is fast. For example, for a GroEL structure (3668 residues, 26957 atoms, 7 chains) it takes only 135 seconds using 1 CPU, and 44 seconds using 10 CPUs. Analogous job takes 3630 seconds using TLSMD server. For a lysozime structure it takes 9.5 seconds with one CPU, and 2.5 seconds using 10 CPUs. The timing results may vary depending on the performance of your computer. There is ongoing work that will slightly improve phenix.find_tls_groups within the next few weeks / a month; however the current version is functional and can be tried now. An example of such improvements are analyzing (scoring) user-defined TLS groups (for example, TLS groups from PDB file header), automated combining cross-chain TLS groups (non-contiguous segments) that will be obtained through connectivity analysis, better handling non-protein chains, and more. Integration with phenix.refine is also planned. Any feedback is very much appreciated! Thanks, Pavel.
Great; look forwards to using, A question for those of us who have been using TLSMD for a few years is how the groups differ. You give timing comparisons for GroEL but do not report if the TLS groups differ, and if they do, how much the groups differ: e.g. is it a residue or two at the group ends, or larger differences. Mark ________________________________________ From: Pavel Afonine [[email protected]] Sent: Tuesday, December 14, 2010 9:45 PM To: PHENIX user mailing list Subject: [phenixbb] phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups PHENIX users: starting dev-610 (development version of PHENIX) there is a new tool available for completely automated partitioning a model into TLS groups: http://www.phenix-online.org/download/nightly_builds.cgi To run: phenix.find_tls_groups model.pdb or if you have a multiple CPU machine: phenix.find_tls_groups model.pdb nproc=N where N is the number of CPUs available (thanks Nat for parallelization!). There is no parameters that a user is supposed to tweak (except defining the number of CPUs, if desired). The result of running the above command are atom selections that define TLS groups. These atom selections are ready to use in phenix.refine. This is available from PHENIX GUI too, where automatically defined TLS groups can be readily visualized and checked on the graphics (thanks Nat!). The algorithm is fast. For example, for a GroEL structure (3668 residues, 26957 atoms, 7 chains) it takes only 135 seconds using 1 CPU, and 44 seconds using 10 CPUs. Analogous job takes 3630 seconds using TLSMD server. For a lysozime structure it takes 9.5 seconds with one CPU, and 2.5 seconds using 10 CPUs. The timing results may vary depending on the performance of your computer. There is ongoing work that will slightly improve phenix.find_tls_groups within the next few weeks / a month; however the current version is functional and can be tried now. An example of such improvements are analyzing (scoring) user-defined TLS groups (for example, TLS groups from PDB file header), automated combining cross-chain TLS groups (non-contiguous segments) that will be obtained through connectivity analysis, better handling non-protein chains, and more. Integration with phenix.refine is also planned. Any feedback is very much appreciated! Thanks, Pavel. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Mark, tomorrow I will a post a link to some detailed description of underlying algorithms and examples. Pavel. On 12/14/10 7:34 PM, Mayer, Mark (NIH/NICHD) [E] wrote:
Great; look forwards to using, A question for those of us who have been using TLSMD for a few years is how the groups differ. You give timing comparisons for GroEL but do not report if the TLS groups differ, and if they do, how much the groups differ: e.g. is it a residue or two at the group ends, or larger differences.
Mark
________________________________________ From: Pavel Afonine [[email protected]] Sent: Tuesday, December 14, 2010 9:45 PM To: PHENIX user mailing list Subject: [phenixbb] phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups
PHENIX users:
starting dev-610 (development version of PHENIX) there is a new tool available for completely automated partitioning a model into TLS groups:
http://www.phenix-online.org/download/nightly_builds.cgi
To run:
phenix.find_tls_groups model.pdb
or if you have a multiple CPU machine:
phenix.find_tls_groups model.pdb nproc=N
where N is the number of CPUs available (thanks Nat for parallelization!). There is no parameters that a user is supposed to tweak (except defining the number of CPUs, if desired).
The result of running the above command are atom selections that define TLS groups. These atom selections are ready to use in phenix.refine.
This is available from PHENIX GUI too, where automatically defined TLS groups can be readily visualized and checked on the graphics (thanks Nat!).
The algorithm is fast. For example, for a GroEL structure (3668 residues, 26957 atoms, 7 chains) it takes only 135 seconds using 1 CPU, and 44 seconds using 10 CPUs. Analogous job takes 3630 seconds using TLSMD server. For a lysozime structure it takes 9.5 seconds with one CPU, and 2.5 seconds using 10 CPUs. The timing results may vary depending on the performance of your computer.
There is ongoing work that will slightly improve phenix.find_tls_groups within the next few weeks / a month; however the current version is functional and can be tried now. An example of such improvements are analyzing (scoring) user-defined TLS groups (for example, TLS groups from PDB file header), automated combining cross-chain TLS groups (non-contiguous segments) that will be obtained through connectivity analysis, better handling non-protein chains, and more. Integration with phenix.refine is also planned.
Any feedback is very much appreciated!
Thanks, Pavel.
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (2)
-
Mayer, Mark (NIH/NICHD) [E] -
Pavel Afonine