[phenixbb] Autobuild iterative omit map error

Terwilliger, Thomas Charles terwilliger at lanl.gov
Fri Feb 20 08:20:53 PST 2015

Hi Emily,

(Back on-list so others can see the answer.)  It seems that your PDB file has a "TER" record between residues ASN 446 and ALA 447 of chain B.  Our parsing system interprets that as the end of chain B and thinks that ALA 447 is another chain.  You can see this by running:

   phenix.print_sequence xxxxx.pdb

I tried deleting the TER record and it looks as though autobuild will get past the interpretation stage with it taken out.

Let me know if that doesn't do it!

(Also...do you know why the TER record might be there?  It is a little surprising!)

All the best,
Tom T

On Feb 20, 2015, at 9:10 AM, Emilia C. Arturo (Emily) wrote:

Thank you Tom!
Attached are the reflections file, sequence file, input model pdb file, and the log file from phenix.

On Fri, Feb 20, 2015 at 11:01 AM, Terwilliger, Thomas Charles <terwilliger at lanl.gov<mailto:terwilliger at lanl.gov>> wrote:
Hi Emily,
I'm sorry for the trouble!  I'll be happy to try and help with it.  If you send me (off-list) the input files you are using and the full log file I'll have a look.
All the best,
Tom T

On Feb 20, 2015, at 7:53 AM, Emilia C. Arturo (Emily) wrote:

> Hello.
> I'd like to use phenix's Autobuild iterative omit map tool, but have run into an error I could use some help with. When the process aborts, the message that phenix outputs is that the input file has duplicate chains. I looked at the pdb file and I do not see duplicate chains; could the ANISOU records for each atom generated by TLS refinement be hanging up the process? I had no error with Autobuild when I started the iterative map process using an input file that had been generated by phenix.refine using the same configuration as the TLS refinement had used (except, of course, for the TLS parameters).
> Thanks for your attention.
> Emily.
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