Hi Joana,
By default it only lists non-trans peptides. Theis command worked for me:
molprobity.omegalyze tempdir/3bwh/pdb3bwh.pdb nontrans_only=False
Cheers,
Robbie
> -----Original Message-----
> From: Joana Pereira <joana.pere...@tuebingen.mpg.de>
> Sent: Friday, September 4, 2020 12:04
> To: Robbie Joosten <robbie_joos...@hotmail.com>;
> CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Omega angles with molprobity
>
> Hi Robbie,
>
> Thanks for the quick response :) That was my first try but it does not list me
> the angles.. see the output below:
>
> Starting molprobity.omegalyze
> on Fri Sep 4 12:00:35 2020 by jpereira
> ===============================================================
> ================
>
> Processing files:
> -------------------------------------------------------------------------------
>
> Found model, xxxx.pdb
>
> Processing PHIL parameters:
> -------------------------------------------------------------------------------
>
> No PHIL parameters found
>
> Final processed PHIL parameters:
> -------------------------------------------------------------------------------
> data_manager {
> model {
> file = "xxxx.pdb"
> }
> default_model = "xxxx.pdb"
> }
>
>
> Starting job
> ===============================================================
> ================
> residues:type:omega:conformation:mc_bmax
> SUMMARY: 0 cis prolines out of 5 PRO
> SUMMARY: 0 twisted prolines out of 5 PRO
> SUMMARY: 0 other cis residues out of 140 nonPRO
> SUMMARY: 0 other twisted residues out of 140 nonPRO
>
> ===============================================================
> ================
>
>
> What I would like to have is a per residue assignment of omega angles, as
> molprobity.ramanalyse does. Of course i could code it, but I was trying to
> avoid that ;)
>
>
> Cheers,
>
> Joana
>
>
>
>
> On 04.09.20 11:45, Robbie Joosten wrote:
>
>
> Hi Joana,
>
> molprobity.omegalyze seems to do what you want. Just run it on the
> command prompt.
>
> Cheers,
> Robbie
>
>
> -----Original Message-----
> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK>
> <mailto:CCP4BB@JISCMAIL.AC.UK> On Behalf Of Joana
> Pereira
> Sent: Friday, September 4, 2020 11:29
> To: CCP4BB@JISCMAIL.AC.UK
> <mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: [ccp4bb] Omega angles with molprobity
>
> 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
>
> --
> Postdoctoral Researcher
> Department of Protein Evolution
>
> Max Planck Institute for Developmental Biology Max-Planck-
> Ring 5
> 72076 Tübingen
> GERMANY
>
>
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> Department of Protein Evolution
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> Max Planck Institute for Developmental Biology Max-Planck-Ring 5
> 72076 Tübingen
> GERMANY
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