Hi, Hopefully I'm just missing something obvious.... I'm trying to copy the Rfree set from an old set of data, to a new mutant structure....and extend to higher resolution. I've tried: phenix.reflection_file_converter old.mtz --label="R-free-flags" new.sca --label="i_obs,sigma" --mtz new.mtz and several other combination, but I am still failing to get phenix to read multiple data files and output the desired mtz. I can get just the Rfree flags or the I and SigI, but not both. I also tried with phenix.refine phenix.refine --dry-run old.pdb old.mtz new.sca ligands.cif refinement.input.xray_data.labels="i_obs,sigma" refinement.input.xray_data.r_free_flags.label="R-free-flags" This seems closer, but I get the error: Sorry: R-free flags not compatible with F-obs array: missing flag for 492 F-obs selected for refinement: Thanks, -bob
Hi Bob, you can use "Reflection file editor" for this. It is available from PHENIX GUI. I'm not sure if the corresponding command line option exists, Nat knows this better. Pavel. On 5/19/10 9:09 AM, Robert Immormino wrote:
Hi,
Hopefully I'm just missing something obvious....
I'm trying to copy the Rfree set from an old set of data, to a new mutant structure....and extend to higher resolution.
I've tried:
phenix.reflection_file_converter old.mtz --label="R-free-flags" new.sca --label="i_obs,sigma" --mtz new.mtz
and several other combination, but I am still failing to get phenix to read multiple data files and output the desired mtz. I can get just the Rfree flags or the I and SigI, but not both.
I also tried with phenix.refine
phenix.refine --dry-run old.pdb old.mtz new.sca ligands.cif refinement.input.xray_data.labels="i_obs,sigma" refinement.input.xray_data.r_free_flags.label="R-free-flags"
This seems closer, but I get the error:
Sorry: R-free flags not compatible with F-obs array: missing flag for 492 F-obs selected for refinement:
Thanks, -bob _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
If it's not implemented already, I'd love to see a command line utility to do this. F On May 19, 2010, at 10:13 AM, Pavel Afonine wrote:
Hi Bob,
you can use "Reflection file editor" for this. It is available from PHENIX GUI. I'm not sure if the corresponding command line option exists, Nat knows this better.
Pavel.
On 5/19/10 9:09 AM, Robert Immormino wrote:
Hi,
Hopefully I'm just missing something obvious....
I'm trying to copy the Rfree set from an old set of data, to a new mutant structure....and extend to higher resolution.
I've tried:
phenix.reflection_file_converter old.mtz --label="R-free-flags" new.sca --label="i_obs,sigma" --mtz new.mtz
and several other combination, but I am still failing to get phenix to read multiple data files and output the desired mtz. I can get just the Rfree flags or the I and SigI, but not both.
I also tried with phenix.refine
phenix.refine --dry-run old.pdb old.mtz new.sca ligands.cif refinement.input.xray_data.labels="i_obs,sigma" refinement.input.xray_data.r_free_flags.label="R-free-flags"
This seems closer, but I get the error:
Sorry: R-free flags not compatible with F-obs array: missing flag for 492 F-obs selected for refinement:
Thanks, -bob _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
On Wed, May 19, 2010 at 9:13 AM, Pavel Afonine
you can use "Reflection file editor" for this. It is available from PHENIX GUI. I'm not sure if the corresponding command line option exists, Nat knows this better.
In a hurry right now, but to summarize: iotbx.reflection_file_editor will do this on the command line, but it's intended as a tool for automation and testing, and is currently undocumented. Something like this should do it: iotbx.reflection_file_editor data.mtz r_free_flags.extend=True but I'd really recommend trying the GUI first. FYI, it assumes that R-free flags were initially generated randomly, not by thin resolution shells (i.e. using DATAMAN or SFTOOLS). -Nat
Hi Robert, Using CCP4... ;-) (maybe Freerflag) you can do it.... David Robert Immormino wrote:
Hi,
Hopefully I'm just missing something obvious....
I'm trying to copy the Rfree set from an old set of data, to a new mutant structure....and extend to higher resolution.
I've tried:
phenix.reflection_file_converter old.mtz --label="R-free-flags" new.sca --label="i_obs,sigma" --mtz new.mtz
and several other combination, but I am still failing to get phenix to read multiple data files and output the desired mtz. I can get just the Rfree flags or the I and SigI, but not both.
I also tried with phenix.refine
phenix.refine --dry-run old.pdb old.mtz new.sca ligands.cif refinement.input.xray_data.labels="i_obs,sigma" refinement.input.xray_data.r_free_flags.label="R-free-flags"
This seems closer, but I get the error:
Sorry: R-free flags not compatible with F-obs array: missing flag for 492 F-obs selected for refinement:
Thanks, -bob _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122
Hi Robert, You can do this really easily in the PHENIX GUI with the reflection file editor. If you want to use a command-line tool you can also use iotbx.r_free_flags_completion_simple. All the best, Tom T On May 19, 2010, at 10:18 AM, David Cobessi wrote:
Hi Robert, Using CCP4... ;-) (maybe Freerflag) you can do it.... David
Robert Immormino wrote:
Hi,
Hopefully I'm just missing something obvious....
I'm trying to copy the Rfree set from an old set of data, to a new mutant structure....and extend to higher resolution.
I've tried:
phenix.reflection_file_converter old.mtz --label="R-free-flags" new.sca --label="i_obs,sigma" --mtz new.mtz
and several other combination, but I am still failing to get phenix to read multiple data files and output the desired mtz. I can get just the Rfree flags or the I and SigI, but not both.
I also tried with phenix.refine
phenix.refine --dry-run old.pdb old.mtz new.sca ligands.cif refinement.input.xray_data.labels="i_obs,sigma" refinement.input.xray_data.r_free_flags.label="R-free-flags"
This seems closer, but I get the error:
Sorry: R-free flags not compatible with F-obs array: missing flag for 492 F-obs selected for refinement:
Thanks, -bob _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
Curious, will either of the utilities (iotbx.reflection_file_editor or iotbx.r_free_flags_completion_simple) follow --use-lattice-symmetry-in- r-free-flag-generation that phenix.reflection_file_converter offers? Thanks F On May 19, 2010, at 10:20 AM, Tom Terwilliger wrote:
Hi Robert, You can do this really easily in the PHENIX GUI with the reflection file editor. If you want to use a command-line tool you can also use iotbx.r_free_flags_completion_simple. All the best, Tom T
On May 19, 2010, at 10:18 AM, David Cobessi wrote:
Hi Robert, Using CCP4... ;-) (maybe Freerflag) you can do it.... David
Robert Immormino wrote:
Hi,
Hopefully I'm just missing something obvious....
I'm trying to copy the Rfree set from an old set of data, to a new mutant structure....and extend to higher resolution.
I've tried:
phenix.reflection_file_converter old.mtz --label="R-free-flags" new.sca --label="i_obs,sigma" --mtz new.mtz
and several other combination, but I am still failing to get phenix to read multiple data files and output the desired mtz. I can get just the Rfree flags or the I and SigI, but not both.
I also tried with phenix.refine
phenix.refine --dry-run old.pdb old.mtz new.sca ligands.cif refinement.input.xray_data.labels="i_obs,sigma" refinement.input.xray_data.r_free_flags.label="R-free-flags"
This seems closer, but I get the error:
Sorry: R-free flags not compatible with F-obs array: missing flag for 492 F-obs selected for refinement:
Thanks, -bob _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http:// solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/ cbss
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
On Wed, May 19, 2010 at 9:50 AM, Francis E Reyes wrote: Curious, will either of the utilities (iotbx.reflection_file_editor or
iotbx.r_free_flags_completion_simple)
follow --use-lattice-symmetry-in-r-free-flag-generation that
phenix.reflection_file_converter offers? Not sure about the second one (it's more or less obsolete at this point),
but iotbx.reflection_file_editor (and the GUI equivalent, and phenix.refine)
have this option turned on by default.
-Nat
Dear phenixbb,
I'm trying to copy an R-free set from one point mutant structure to my
new data. This had worked previously using the GUI, inputting the
.sca for the new set and the .mtz from the reference data.
For my newest mutant I'm getting the error message:
The unit cell for the Miller array blah/blah:R-free-flags (53.445,
53.547, 161.082, 90, 90, 90) is significantly different than the
output unit cell (54.033, 53.731, 161.804, 90, 90, 90).
Is this difference actually too big to be using the same R-free set?
If the difference is not too big, how do I get the reflection file
editor past this error?
-bob
On Wed, May 19, 2010 at 2:52 PM, Ralf W. Grosse-Kunstleve
Curious, will either of the utilities (iotbx.reflection_file_editor or iotbx.r_free_flags_completion_simple) follow --use-lattice-symmetry-in- r-free-flag-generation that phenix.reflection_file_converter offers?
Yes.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Mon, Jun 21, 2010 at 11:53 AM, Robert Immormino
Is this difference actually too big to be using the same R-free set? If the difference is not too big, how do I get the reflection file editor past this error?
Sorry, this has been an item on my to-do list for a while. The next installer will have options to disable the unit cell (or space group) check (in the "Change symmetry" dialog). I need to test the new code on something real, so if you're willing to send me (not the list!) the files, I can give you the combined reflections. There probably are situations where these unit cells are different enough to cause problems (MIR, or switching to new data partway through refinement), but I would definitely want to keep using the same R-free set in this case. thanks, Nat
participants (7)
-
David Cobessi -
Francis E Reyes -
Nathaniel Echols -
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
Robert Immormino -
Tom Terwilliger