Hi all !! I am using phenix.refine to refine my 3.2 A structure. Also i use xtal_pdbsubmission utility in CNS to generate pdb file which is submission ready format. Please note no refinement in CNS only formating. Phenix.refine gave a R and Rfree of 0.1929 & 0.2512 ( rmsd bonds = 0.006) respectively. When i format in CNS it gave R and Rfree 0.2282 & 0.2794 ( rmsd bonds= 0.010865 ). Am i doing any mistake ?? As for as i know we cant generate a submission ready PDB format from phenix.refine. Is it possible to implement it, which will be very helpful for all of us. Thanks in advance for your inputs regards John
Hi John,
Phenix.refine gave a R and Rfree of 0.1929 & 0.2512 ( rmsd bonds = 0.006) respectively. When i format in CNS it gave R and Rfree 0.2282 & 0.2794 ( rmsd bonds= 0.010865 ). Am i doing any mistake ??
Probably not. My guess is the difference is due to the bulk-solvent correction.
As for as i know we cant generate a submission ready PDB format from phenix.refine. Is it possible to implement it, which will be very helpful for all of us.
This is an ongoing project. We are doing some things differently than other programs which requires discussions and adjustments at both ends, PDB and us. The phenix.refine PDB files contain almost everything the PDB needs but they don't have the right tools to process this information. Since phenix.refine is new there haven't been many submissions yet, so the PDB hasn't had a big incentive to invest time (i.e. money) to adjust the software at their end. Since it is difficult to submit phenix.refine results, people run refmac or cns to prepare for submission, which makes the PDB happy but doesn't solve the problem. This is a bit of a chicken and egg problem. Maybe if you also try refmac to see if the R-factors are better, then submit whatever gives the best results, but also tell the PDB that you'd much rather deposit the phenix.refine files directly, you'd hopefully have a smooth deposition process but also make the PDB understand that something needs to be done to help people who used phenix.refine. Ralf
Hi, Regarding to the issue of easy PDB deposition, we do have a program called pdb-extract which extracts the complete information from both the LOG file and from the header of the pdb file generated by 35 crystallographic programs/packages including Phenix. So far, only the extracted TLS information from Phenix can not be converted by ADIT during deposition. I believe this will be resolved soon. The web page of pdb_extract is http://pdb-extract.rcsb.org/ The new version http://pdb-ws-29.rutgers.edu/pdb-extract/prog/pdb-extract-v3.0-prod.tar.gz Please try the version 3.0 of pdb_extract and let me know for any problems. Thanks. Regards, Huanwang
Hi John,
Phenix.refine gave a R and Rfree of 0.1929 & 0.2512 ( rmsd bonds = 0.006) respectively. When i format in CNS it gave R and Rfree 0.2282 & 0.2794 ( rmsd bonds= 0.010865 ). Am i doing any mistake ??
Probably not. My guess is the difference is due to the bulk-solvent correction.
As for as i know we cant generate a submission ready PDB format from phenix.refine. Is it possible to implement it, which will be very helpful for all of us.
This is an ongoing project. We are doing some things differently than other programs which requires discussions and adjustments at both ends, PDB and us.
The phenix.refine PDB files contain almost everything the PDB needs but they don't have the right tools to process this information. Since phenix.refine is new there haven't been many submissions yet, so the PDB hasn't had a big incentive to invest time (i.e. money) to adjust the software at their end. Since it is difficult to submit phenix.refine results, people run refmac or cns to prepare for submission, which makes the PDB happy but doesn't solve the problem. This is a bit of a chicken and egg problem.
Maybe if you also try refmac to see if the R-factors are better, then submit whatever gives the best results, but also tell the PDB that you'd much rather deposit the phenix.refine files directly, you'd hopefully have a smooth deposition process but also make the PDB understand that something needs to be done to help people who used phenix.refine.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi John, we are working on a deposition header for the PDB files. The R-factor differences you see between phenix.refine and CNS are probably because of differences in the bulk solvent model (or TLS if you used it). The differences in the bond rmsd is a result of a bug in the reporting of these numbers in phenix.refine. If you obtain the latest version (d7) of the phenix prerelease this problem should be fixed. Cheers, Paul john kryst wrote:
Hi all !!
I am using phenix.refine to refine my 3.2 A structure. Also i use xtal_pdbsubmission utility in CNS to generate pdb file which is submission ready format. Please note no refinement in CNS only formating.
Phenix.refine gave a R and Rfree of 0.1929 & 0.2512 ( rmsd bonds = 0.006 ) respectively. When i format in CNS it gave R and Rfree 0.2282 & 0.2794 ( rmsd bonds= 0.010865 ). Am i doing any mistake ??
As for as i know we cant generate a submission ready PDB format from phenix.refine. Is it possible to implement it, which will be very helpful for all of us.
Thanks in advance for your inputs
regards John
------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Paul Adams Senior Staff Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
Hi John, john kryst wrote:
Phenix.refine gave a R and Rfree of 0.1929 & 0.2512 ( rmsd bonds = 0.006 ) respectively. When i format in CNS it gave R and Rfree 0.2282 & 0.2794 ( rmsd bonds= 0.010865 ). Am i doing any mistake ??
The difference in R-factors is because of the following (at least): 1) Different bulk-solvent modeling (targets, protocols) (currently we have the most sophisticated algorithm); 2) Different anisotropic scaling protocol (tightly integrated with the bulk-solvent modeling); 3) Different mask calculation parameters; 4) Different way of TLS handing (if used at all in your case); 5) Different form-factors values; 6) If you use H atoms, other programs may have their specific ways of treating them at input; .... I can make an endless list of why the values can be different. Certainly, the bulk-solvent and anisotropic scaling are two the most probable candidates for making this difference. In general, I would NEVER use another program to generate statistics file. Even not because different programs produces slightly different results (which is normal), but because there are myriads of subtle parameters that needs to be taken care of and adjusted to PROPERLY reproduce a result when transferring from one program to another. Otherwise you are bound to end up with the difference in numbers like you got. As a temporary work around I would just get a template PDB file header and copy in necessary numbers from the output phenix.refine file. As for the different stereo-chemistry statistics values (bonds, angles): we recently discovered that we were printing out different values from what the users normally expect to see (I wouldn't call it a bug, though). Previously we we printing mean errors. We corrected it and now we print rmsd values, as people expect. Please get the latest PHENIX to have this fix. Pavel.
Hi all !!! Thanks a lot to all of you for your suggestions... As many of you have guessed it is a problem of Bulk solvent correction. When i generated the pdb file using 0 cycles, the values are very much comparable with phenix.refine. Interestingly CNS-1.2 xtal_pdbsubmission gave the same result as phenix.refine. which once again confirms that its a bulk solvent correction problem. As Huanwang suggested, pdb_extract could generate submission ready cif file. Once again thanks to all of you... But still i have problem with rmsd_bonds. I am using phenix.refine version 2007_05_29_2026 . Refmac gave rmsd_bonds 0.009 and rmsd_angles1.211 but phenix gave rmsd_bonds 0.006 & rmsd_angles 0.793. regards John
Hi John, you should probably download the latest prerelease of PHENIX (d7), from the web page. This contains a version of phenix.refine from early July. Cheers, Pau' On Jul 30, 2007, at 10:05 AM, john kryst wrote:
Hi all !!!
Thanks a lot to all of you for your suggestions... As many of you have guessed it is a problem of Bulk solvent correction. When i generated the pdb file using 0 cycles, the values are very much comparable with phenix.refine. Interestingly CNS-1.2 xtal_pdbsubmission gave the same result as phenix.refine. which once again confirms that its a bulk solvent correction problem.
As Huanwang suggested, pdb_extract could generate submission ready cif file.
Once again thanks to all of you... But still i have problem with rmsd_bonds. I am using phenix.refine version 2007_05_29_2026 . Refmac gave rmsd_bonds 0.009 and rmsd_angles1.211 but phenix gave rmsd_bonds 0.006 & rmsd_angles 0.793.
regards John _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Paul Adams Senior Staff Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
participants (5)
-
hyang＠rcsb.rutgers.edu -
john kryst -
Paul Adams -
Pavel Afonine -
Ralf W. Grosse-Kunstleve