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
[email protected]
or 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 : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Fri, Sep 4, 2020 at 5:35 AM Tim Gruene <[email protected]> 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 <[email protected]> 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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