[phenixbb] Phenix Ligand Identification error

Nathaniel Echols nechols at lbl.gov
Sat Apr 24 06:46:44 PDT 2010

On Sat, Apr 24, 2010 at 3:19 AM, Rajan <rajanvyas at gmail.com> wrote:

> I was searching for a ligand present in the active site of my protein using
> Ligand  Search in  "PHENIX"
> but i stuck in between with an error :
> AttributeError : ligand_identification instance has no attribute
> 'connections'
>   File
> "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py",
> line 1454, in Run
>     return self.connections['STOP ']
> Please let me know if some one can identify the problem, i don't know
> whether it is a bug or problem in my files.

Possibly both.  The error message is definitely a bug - I'll make sure the
appropriate person gets this.  It may have already been fixed, because the
most current code is obviously different than what's in 1.6.1, so it might
be worth trying the latest nightly build.  I just put last night's installer
online; it should be relatively stable.

However, the reason it stopped at that point in the code was possible an
input problem:

        print 'Resolve failed to make difference map in Step 1.\n'
        print '!!!!!Please double-check mtz labin assignment.!!!!!\n'

So it might not be able to use the data you're providing it - impossible to
tell why from here.

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