Re: [phenixbb] Problem with Autobuild

Hi Jobi, I think that your helices_strands.pdb is a CA-only trace. If so, then it is true that autobuild cannot make use of it. My guess is that helices_strands.pdb came from phenix.find_helices_strands mymap.mtz which will produce a CA trace using the trace_chain algorithm. Can you possibly try instead: phenix.find_helices_strands trace_chain=False mymap.mtz which will do more of what you want. I am thinking of changing the default back to "trace_chain=False" so that you won't be misled in the future... All the best, Tom T

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Dear Ralf, Please see the result from hierarchy run.

phenix.pdb.hierarchy helices_strands .pdb file helices_strands.pdb total number of: models: 1 chains: 1 alt. conf.: 0 residues: 540 atoms: 540 anisou: 0 number of atom element+charge types: 1 histogram of atom element+charge frequency: " " 540 residue name classes: "common_amino_acid" 540 number of chain ids: 1 histogram of chain id frequency: " " 1 number of alt. conf. ids: 0 number of residue names: 1 histogram of residue name frequency: "GLY" 540

Thanks. Jobi

On Wed, Jan 12, 2011 at 2:04 PM, Ralf W. Grosse-Kunstleve wrote:

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I'm guessing the helices_strands.pdb file got corrupted somehow. Does

phenix.pdb.hierarchy helices_strands.pdb

give clues?

Ralf

*From:* Jobichen Chacko *To:* PHENIX user mailing list *Sent:* Tue, January 11, 2011 8:50:09 PM *Subject:* [phenixbb] Problem with Autobuild

Dear All, I am trying to run Phenix autobuild using the helices-strands.pdb obtained using find helices and strands program. But the program is not running with the following error message. The file helices_strands.pdb does not seem to be a PDB file

Thanks. Jobi

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