[ccp4bb] wich program to test an alternative phaser solution
Dear all, We have a phaser output with 2 alternative solutions. Not differing much by the statistics. Phaser provides the solution with the highest LLG. However I am not convinced by that solution. What program should be used with the input PDB and the Euler angles and translation parameters (found in the .sol file) to generate the alternative solution? Thank you in advance, Fred.
Re: [ccp4bb] wich program to test an alternative phaser solution
PDBSET xyzin model.pdb ROTA EULER a b c SHIFT FRAC tx ty tz CELL new cell end Vellieux wrote: Dear all, We have a phaser output with 2 alternative solutions. Not differing much by the statistics. Phaser provides the solution with the highest LLG. However I am not convinced by that solution. What program should be used with the input PDB and the Euler angles and translation parameters (found in the .sol file) to generate the alternative solution? Thank you in advance, Fred.
Re: [ccp4bb] wich program to test an alternative phaser solution
Hi Fred, in future PHASER runs you can also ask the program to write out an X number of the top solutions as separate coordinate files via the keyword TOPFILES (e.g 'TOPFILES 10' for the top ten solutions). In the PHASER GUI you can enter that request in the 'Define Data' block. best wishes, Savvas Savvas N. Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19 Email: [EMAIL PROTECTED] http://www.eiwitbiochemie.ugent.be/units_en/structbio_en.html -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Vellieux Sent: Tuesday, January 15, 2008 10:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] wich program to test an alternative phaser solution Dear all, We have a phaser output with 2 alternative solutions. Not differing much by the statistics. Phaser provides the solution with the highest LLG. However I am not convinced by that solution. What program should be used with the input PDB and the Euler angles and translation parameters (found in the .sol file) to generate the alternative solution? Thank you in advance, Fred.
Re: [ccp4bb] wich program to test an alternative phaser solution
As suggested earlier, you can use the TOPFILES command to get Phaser to produce the files for more solutions. However, instead of rerunning the whole job, you can produce the PDB files alone by feeding the .sol file into a packing (MR_PAK) job, or both PDB and MTZ files by feeding the .sol file into a rescoring (MR_LLG) job. Randy Read On Jan 15 2008, Vellieux wrote: Dear all, We have a phaser output with 2 alternative solutions. Not differing much by the statistics. Phaser provides the solution with the highest LLG. However I am not convinced by that solution. What program should be used with the input PDB and the Euler angles and translation parameters (found in the .sol file) to generate the alternative solution? Thank you in advance, Fred.
