[ccp4bb] Qt-PISA not recognizing Trp H bond

[Engin Özkan]

Hi,

I have a question about QtPISA that ships with the latest ccp4 
(7.1.003). Analyzing one of our recent structures, I came across what 
appears to be a hydrogen bond at a protein-protein interface, but it is 
not being picked by QtPISA (built from PISA v 2.1.2). It is a 2.9 Å 
(donor to acceptor) distance between the Trp side chain Nitrogen and a 
main chain carbonyl oxygen.


See https://www.dropbox.com/s/yebyomdqu9ukjys/coot.png?dl=0

The N-H...O angle is 134 degrees (after adding hydrogens with 
phenix.reduce), and while that is not great, it is not horrible. 
Artificially changing the angle to >160 degrees did not make PISA detect 
the hydrogen bond.


I thought that maybe PISA ignored Trp side chains altogether, but an 
earlier version running on PDBe's webpage (v. 1.52) reports this H bond 
using the identical pdb file as input.


So, it appears that the developers removed the detection of these close 
contacts as hydrogen bonds at some point between versions 1.52 and 
2.1.2. Could anyone help me explain this, or what I might be doing wrong 
here?


Thank you,

Engin

P.S. The source code or a version history may be available somewhere to 
check this, but the CCP4 page is down, and I don't know where to look.


--
Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
http://voices.uchicago.edu/ozkanlab



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Re: [ccp4bb] diffdump in CCP4 7.1

[David Waterman]

Dear Jan,

If you just want to generate XDS input files then Tim's suggestion of using
generate_XDS.INP is exactly right. If you or others miss the functionality
of diffdump in CCP4 for reading image headers, then I suggest this command
as a replacement:

dials.show /path/to/image_file

This is available at the command line with a CCP4 environment set up.

Cheers
-- David


On Sat, 22 Aug 2020 at 01:48, Tim Gruene  wrote:

> Dear David,
>
> Kay Diederich's generate_XDS.INP
>
> https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP
> creates the full XDS.INP for you for a large number of frame formats.
> It is not CCP4, but I think there are no restrictions for using it.
>
> Best regards,
> Tim
>
> On Fri, 21 Aug 2020 14:29:26 -0700
> Jan Abendroth  wrote:
>
> > Hi all,
> >
> > It looks as if the utility ‘diffdump’ is no longer part of the
> > standard linux CCP4 7.1 distribution.
> >
> > It has been a very handy tool for preparing XDS input files.
> >
> > Does anyone know if there is an equivalent script in CCP4 7.1?
> >
> >
> >
> > Thanks,
> >
> > Jan
> >
>
>
>
>
> --
> --
> 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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