[phenixbb] Few questions -- FreeR flag specification

Tom Terwilliger terwilliger at lanl.gov
Thu Mar 15 11:58:49 PDT 2007

Hi John,
I'm sorry for the slow reply; I was on a site visit and out of email contact.

The AutoBuild wizard in the current version (which I am afraid you 
probably do not have!) does try to take the FreeR flags from your 
input file. You can also tell it specifically to do so with the GUI 
and in the command-line with

input_refinement_labels="FP SIGFP None None None None None None FreeR"

If you have version 1.25a , then you still should be able to specify 
the column for FreeR flags in the GUI window that asks which column 
labels to use (I could be wrong about that, however, as I don't have 
this version on my computer any longer).

You should also be able to specify them with a script:

phenix.runWizard AutoBuild AutoBuild.start_from_model

terwill at rosie> cat 
#            AutoBuild.start_from_model
#            script to run a AutoBuild starting from a model
#                   Version 1.26 of 26-Jan-2007
#            run with:
#   phenix.runWizard AutoBuild AutoBuild.start_from_model [restart]
#            if you specify restart it will forget everything,
#               otherwise it will continue on from where it is now.

input_ncs_file  NONE                 # heavy-atom or PDB file for finding NCS
input_data_file $PHENIX/examples/p9-sad/solve_1.mtz  # file with 
experimental data.
#  Can be any format if only FP SIGFP; must be mtz if phases or HL or 
FreeR input
input_labels  FP SIGFP None None None None None None  FreeR_flag  # optional
            # line defining the 9 columns in input_mtz_file corresponding to
            #  FP SIGFP PHIB FOM HLA HLB HLC HLD FreeR  (use "None" 
for missing)

input_map_file $PHENIX/examples/p9-sad/resolve_1.mtz  # Optional 
map-coefficients file for first rebuild
input_map_labels  FP PHIM FOMM       # optional line defining the 3 columns
            # in input_map_file corresponding to FP PHIB FOM ("None" 
for missing)
input_seq_file $PHENIX/examples/p9-sad/seq.dat  # file with sequence 
in 1-letter form
                                         # separate chains with >>>
resolution 2.5                          # high-resolution limit
solvent_fraction 0.60

# you can put any other parameters here

  input_pdb_file  $PHENIX/examples/p9-sad/p9.pdb # input PDB file for 
  rebuild_in_place True                 # rebuild my_model.pdb in place
                                        # (as opposed to building from scratch)
start_chains_list 4     # chain 1 starts at residue 4

# rebuild residues 21-27 of chain "" and  31-42 of chain ""
# rebuild_res_start_list 21  31
# rebuild_res_end_list 27 42
# rebuild_chain_list  "" ""

# n_cycle_rebuild_min 5
# n_cycle_rebuild_max 10

#  AutoBuild will run automatically from here on with no more inputs

I hope that helps!  The new version of PHENIX that will be out very 
soon fixes many other problems as well!

All the best,
Tom T

At 03:26 AM 3/13/2007, john kryst wrote:
>Hi phenixbb !!
>          I have few questions.
>1. Is there any utility in phenix to write out pdb formatted (which 
>is ready to deposit) output file.. like xtal_pdbsubmission utility in CNS.
>2. In Autobuild wizard how to ask the program to use the Free R 
>flags present in the file. It always generates new Free R flags 
>during refinement.
>One general question.
>Does the rmsd estimation (for eg. rmsd_bonds ) depends on the 
>program we use ??
>I have been refining in CNS. then i used Autobuild wizard to build 
>my model. when i went back to cns the rmsd of bond increased ( 
>0.0218 A). But phenix.refine says it it 0.007A.
>Thanks in advance for your kind inputs.
>phenixbb mailing list
>phenixbb at phenix-online.org

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
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

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