<div dir="ltr">Dear Oliver,<div><br></div><div>Thank you for the bug report. I have fixed the issue with ramachandran restraints and they should be working in the next available nightly build (after dev-2009). </div><div><br></div>Regarding secondary structure: User notes for dev-1999: Parameters for secondary structure restraints moved to pdb_interpretation scope. Old parameter files will not be suitable for secondary structure restraints definitions.<br><br><div>Therefore since dev-1999, please use the following parameter:</div><div>secondary_structure.enabled=True</div><div><br></div><div>If you encounter other problems, please get back to us.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Apr 10, 2015 at 6:46 AM, Oliver Clarke <span dir="ltr"><<a href="mailto:olibclarke@gmail.com" target="_blank">olibclarke@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Also (possibly related?) when I add the parameter "main.secondary_structure_restraints=True” to the command line, I get an error stating that this parameter does not exist, which is weird, because I’m sure that worked previously.<br>
<span class="HOEnZb"><font color="#888888"><br>
Oliver.<br>
</font></span><div class="HOEnZb"><div class="h5">> On Apr 10, 2015, at 9:29 AM, Oliver Clarke <<a href="mailto:olibclarke@gmail.com">olibclarke@gmail.com</a>> wrote:<br>
><br>
> Hi all,<br>
><br>
> When I attempt to run a refinement using phenix.refine from the command line, using the parameter “ramachandran_restraints=true”, in the latest nightly build of phenix (dev-2006), I get the following error:<br>
><br>
> ========================== Anomalous scatterer groups =========================<br>
><br>
> All atoms refined with f_prime=0 and f_double_prime=0.<br>
> Traceback (most recent call last):<br>
> File "/Applications/phenix-dev-2006/build/../modules/phenix/phenix/command_line/refine.py", line 11, in <module><br>
> command_line.run(command_name="phenix.refine", args=sys.argv[1:])<br>
> File "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/command_line.py", line 96, in run<br>
> master_params=customized_master_params)<br>
> File "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/driver.py", line 272, in __init__<br>
> secondary_structure_manager=self.sec_str,<br>
> AttributeError: refine instance has no attribute 'sec_str'<br>
><br>
><br>
> This happens for two different structures, so I don’t think it is a structure-specific thing, and I don’t recall this happening in older builds of phenix. The refinement runs fine if I don’t specify ramachandran restraints. Is there something obvious I am doing wrong?<br>
><br>
> Best,<br>
> Oliver.<br>
><br>
<br>
<br>
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