[buster-discuss] pdb2tls issue

[Clemens Vonrhein]

Dear Marco,

thank you for bringing this to our attention - we hadn't noticed this
yet.

This is due to an incompatibility between GNU awk (as used on Linux
systems and older OS X versions) and BSG awk (as used on newer OS X
systems).

It will be fixed in the next release, now that we have been able to
reproduced it.

Thank you again for sending that clear and edtailed report!

Cheers

Clemens

On Wed, Jul 08, 2015 at 06:03:02PM +0200, Marco Bellinzoni wrote:
> Dear all,
> 
> I've been encountering a problem with pdb2tls within the latest
> autoBUSTER (June 16 release) installation on my Mac Pro running
> Yosemite 10.10.4. I actually had this problem with my oldest
> installation as well. When launching it through
> 
> pdb2tls -p refine.pdb -o test.tls
> 
> I get:
> 
> awk: syntax error at source line 247 in function selection2set
>  context is
>      >>> delete( <<< arr)
> awk: illegal statement at source line 248 in function selection2set
> awk: illegal statement at source line 248 in function selection2set
> 
>  WARNING : ... something went wrong during extraction of TLS
>            parameters. See above.
> 
> Although this does not make BUSTER to stop, when I run it with the
> -TLS option on an input pdb coming out from a previous run with
> user-specified TLS groups, BUSTER does not parse the TLS groups in
> the input pdb, issues a warning message ("WARNING : unable to
> extract available TLS information from REMARK 3 section of....",
> nevertheless followed by "NOTE : using automatic TLS definitions
> based on input PDB file) and simply carries on with the refinement
> after applying the default TLS definitions (one group per chain).
> If I supply TLS definitions in an input file after the -TLS option,
> everything is fine.
> 
> Has anybody else noticed this?
> 
> Thanks,
> Marco
> 
> -- 
> ================================
> Marco Bellinzoni
> Unité de Microbiologie Structurale
> Institut Pasteur
> 25, rue du Dr. Roux
> 75724 Paris Cedex 15
> France
> Tel. +33 (0)1 45688608
> Fax. +33 (0)1 45688604
> ================================
> 
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-- 

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* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
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