[phenixbb] Problem with Autobuild

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Jan 12 06:36:42 PST 2011


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

>> 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
>> <rwgk at yahoo.com>wrote:
>>
>>> I'm guessing the helices_strands.pdb file got corrupted somehow.
>>> Does
>>>
>>> phenix.pdb.hierarchy helices_strands.pdb
>>>
>>> give clues?
>>>
>>> Ralf
>>>
>>>
>>> *From:* Jobichen Chacko <jobichenc at gmail.com>
>>> *To:* PHENIX user mailing list <phenixbb at phenix-online.org>
>>> *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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>>>
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