Hi Bärbel,


this is really helpful - thanks!

Molprobity is one of the programs which PSVS runs anyway, so a server direct for that is useful. It can deal with ensembles, but lots of the stats seem to be provided for each model individually with no average values reported which is a shame. It provides Ramachandran plots which is a also a good alternative to Procheck/Cing.


So, although I prefer Cing and PSVS, in their absence this will be a useful tool.


Thanks again,

Vicky


From: CcpNmr software mailing list <[log in to unmask]> on behalf of Bärbel Blaum <[log in to unmask]>
Sent: 15 October 2018 19:35:35
To: [log in to unmask]
Subject: Re: Validation Servers
 
Dear Vicky,

I have not looked at NMR structures lately but what is much more 
helpful than the pdb validation tool is Molprobity 
http://molprobity.biochem.duke.edu/. We use it a lot in 
crystallography to check 'the physics' and I think in this aspect it 
should be helpful for NMR structures, too. I just noted it explicitly 
mentions NMR structures as well

http://molprobity.biochem.duke.edu/index.php?MolProbSID=qvjlatk5dff42n81kk6m2rge93&eventID=17

so I guess it should be able to deal with ensembles.

I'd be interested to know which websites or tools you find useful in the end!

Best wishes,

Bärbel




Zitat von Victoria Higman-Davies <[log in to unmask]>:

> Hello,
>
>
> I'm struggling to find a functional NMR structure Validation server.
>
>
> Running CING direct from Analysis gives me the following error:
>
> Connection to server URL 
> https://nmr.le.ac.uk/icing/icing/serv/iCingServlet failed with reason:
>
> [SSL:SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure 
> (_ssl.c:581)
>
>
> Is this likely to be a problem at my end or the CING end?
>
>
> Going to the iCing website doesn't seem to work either.
>
> And the PSVS website also seems to be down.
>
>
> How are other people validating their structures at the moment? I 
> tried the PDB validation server, but the report is not very helpful. 
> Do I need to start installing Procheck etc. locally?
>
>
> Thanks,
>
>
> Vicky
>
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--
Bärbel Blaum, Ph.D.
Interfakultäres Institut für Biochemie (IFIB)
Hoppe-Seyler-Strasse 4
D-72076 Tübingen
Germany
+49 70 71 29 733 48
Raum 311

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