Dear all,
Many thanks for such a great and quick feedback! Indeed, I forgot to run
molprobity.omegalyze without input, and I am bit ashamed of that *insert
blushed emoji here*. But now I can do what I was looking for and I am very
grateful for your input :)
Best wishes,
Joana
> On 4. Sep 2020, at 19:35, Nigel Moriarty <nwmoria...@lbl.gov> wrote:
>
> Joana
>
> The developers of molprobity.omegalyze have tried to make their tool easy to
> use and understand by providing lots of help if you type the command without
> inputs. This is a common technique that command line tools employ to provide
> documentation.
>
> > molprobity.omegalyze
> usage: molprobity.omegalyze [-h] [--show-defaults [{0,1,2,3}]]
> [--attributes-level [{0,1,2,3}]] [--write-data]
> [--write-modified] [--write-all] [--overwrite]
> [--citations [{default,cell,iucr}]]
> [files [files ...]] [phil [phil ...]]
>
> -------------------------------------------------------------------------------
> molprobity.omegalyze file.pdb [params.eff] [options ...]
>
> Options:
>
> model=input_file input PDB or mmCIF file
> nontrans_only=True only print nontrans residues (does not affect
> kinemage)
> text=True verbose colon-delimited text output (default)
> kinemage=False Create kinemage markup (overrides text output)
> help = False Prints this help message if true
>
> text output is colon-delimited and follows the format:
> residue:type:omega:conformation
> 'residue' is a unique residue identifier
> 'type' is either proline or general case
> 'omega' is the calculated omega dihedral for the peptide between this
> residue and the preceeding residue
> 'conformation' is: cis for omega within 30 degrees of planar cis
> trans for omega within 30 degrees of planar trans
> twisted for omega not within 30 degrees of planar
>
> SUMMARY statistics provide:
> counts of cis prolines and twisted prolines relative to total prolines
> with
> measurable omega dihedrals across all chains
> counts of non-proline cis and twisted peptides relative to total
> non-proline
> peptides with measurable omega dihedrals across all chains
>
> Cis Prolines occur in ~5% of prolines (1 in 20) at high resolution
> Non-Proline Cis residues occur in ~0.05% of residues (1 in 2000) and require
> clear support from experimental data or homology.
> Twisted peptides are even less frequent and are highly suspect without
> high-resolution data.
>
> Example:
>
> molprobity.omegalyze model=1ubq.pdb kinemage=True
> -------------------------------------------------------------------------------
>
> positional arguments:
> files Input file(s) (e.g. model.cif)
> phil Parameter(s) (e.g. d_min=2.0)
>
> optional arguments:
> -h, --help show this help message and exit
> --show-defaults [{0,1,2,3}], --show_defaults [{0,1,2,3}]
> show default parameters with expert level (default=0)
> --attributes-level [{0,1,2,3}], --attributes_level [{0,1,2,3}]
> show parameters with attributes (default=0)
> --write-data, --write_data
> write DataManager PHIL parameters to file
> (omegalyze_data.eff)
> --write-modified, --write_modified
> write modifed PHIL parameters to file
> (omegalyze_modified.eff)
> --write-all, --write_all
> write all (modified + default + data) PHIL parameters
> to file (omegalyze_all.eff)
> --overwrite overwrite files, this overrides the output.overwrite
> PHIL parameter
> --citations [{default,cell,iucr}]
> show citation(s) for program in different formats
>
> -------------------------------------------------------------------------------
> For additional help, you can contact the developers at
> cctb...@phenix-online.org <mailto:cctb...@phenix-online.org>
> or https://github.com/cctbx/cctbx_project
> <https://github.com/cctbx/cctbx_project>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
> Fax : 510-486-5909 Web : CCI.LBL.gov <http://cci.lbl.gov/>
>
> On Fri, Sep 4, 2020 at 5:35 AM Tim Gruene <tim.gru...@univie.ac.at
> <mailto:tim.gru...@univie.ac.at>> wrote:
> Hi Joana,
>
> unless you are constrained to a molprobity tool, you could use the CCP4
> program ANGLES to list the omega angle for each residue. See
> $CEXAM/unix/runnable/angles.exam
> for an example.
>
> Best,
> Tim
>
>
> On Fri, 4 Sep 2020 11:28:47 +0200
> Joana Pereira <joana.pere...@tuebingen.mpg.de
> <mailto:joana.pere...@tuebingen.mpg.de>> wrote:
>
> > Dear all,
> >
> > Does anyone know which molprobity tool in ccp4/bin lists the omega
> > angles for each residue? I see Phenix provides a comprehensive
> > validation based on Molprobity and, from what I understand, lists the
> > omega angles for each residue. However, I am having troubles to find
> > which molprobity tool provides that info. Any idea?
> >
> > Many thanks!
> >
> > Best wishes
> >
> > Joana Pereira
> >
>
>
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
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