[buster-discuss] pdb2tls issue

Marco Bellinzoni marco.bellinzoni at pasteur.fr
Wed Jul 8 18:03:02 CEST 2015

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?


Marco Bellinzoni
Unité de Microbiologie Structurale
Institut Pasteur
25, rue du Dr. Roux
75724 Paris Cedex 15
Tel. +33 (0)1 45688608
Fax. +33 (0)1 45688604

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