[phenixbb] phenix.phaser params.eff labin problem

G Y gysubscribe at gmail.com
Mon Jul 25 08:03:02 PDT 2011


Hi Nat,

Thanks for you help. I solved that problem with Ralf's help now. Just reset
the $PATH make phenix.phaser appearing before CCP4's.

GP

On Wed, Jul 20, 2011 at 8:39 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> I think this is a known problem, but I'm not sure how to fix it - I am
> downloading the latest CCP4 now to try for myself.  Ralf probably
> knows more.  Did you source the setup file in the CCP4 installation?
>
> -Nat
>
> On Wed, Jul 20, 2011 at 11:35 AM, G P <gysubscribe at gmail.com> wrote:
> > Hi Nat,
> > Thank you so much! That's cool. I just wrote a None to that solution and
> it
> > works!! Now I have some new problems:
> > At beginning, I only have phenix installed. I do not have CCP4 installed.
> > Then I run "phenix.phaser params.eff" to call phenix run phaser from
> script
> > params.eff. It works well.
> > Then, I installed CCP4 with its own phaser inside. Then I run again
> > "phenix.phaser params.eff". The computer start to import files (should be
> > some libraries and supporting files, not input data) from CCP4
> installation
> > directory. It seems so strange for me.
> > And because some of the .so files in CCP4 directory are for 32bit,
> > phenix.phaser gave me error message: wrong ELF class: ELFCLASS32 and
> refused
> > to keep running.
> > Is there anyway to set some kind of PATH variables to let phenix.phaser
> > params.eff run like without CCP4 installed. (which I did at beginning).
> > Sorry for so many questions. Don't worry to reply if you do not have
> time.
> > I fully understand and thanks a lot for your reply.
> > regards,
> > GP
> >
> >
> > On Wed, Jul 20, 2011 at 8:27 PM, Nathaniel Echols <nechols at lbl.gov>
> wrote:
> >>
> >> On Wed, Jul 20, 2011 at 3:46 AM, G P <gysubscribe at gmail.com> wrote:
> >> > Now I can make it. I just type labin="FP,SIGFP,DANO,SIGDANO". Then
> there
> >> > is
> >> > no error to find the labels. I think because I should give all columns
> >> > together.
> >>
> >> Right, sorry, that's another thing that CCTBX does automatically.
> >> This command will show you what array labels Phenix recognizes:
> >>
> >> iotbx.reflection_file_reader data.mtz
> >>
> >> > But there is another problem. When I run the script, it shows me:
> >> > ...
> >> > File
> >> >
> "/usr/local/phenix-1.7.1-743/phaser/phaser/phenix_interface/driver.py",
> >> > line 694, in __init__
> >> >     assert os.path.isfile(params.phaser.solution)
> >> > AssertionError
> >> > File
> >> >
> "/usr/local/phenix-1.7.1-743/phaser/phaser/phenix_interface/driver.py",
> >> > line 694, in __init__
> >> >     assert os.path.isfile(params.phaser.solution)
> >> > AssertionError
> >>
> >> Look for a parameter called "solution" - this needs to be left as
> >> None.  (I don't think there's any way to use this from the command
> >> line right now - it's very specific to the GUI.)
> >>
> >> -Nat
> >> _______________________________________________
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> >> phenixbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >
> >
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> >
> >
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