[phenixbb] Run time error while refining

Subhani Bandara ramssb17 at gmail.com
Fri Jun 22 10:04:10 PDT 2012


Hi Jeff,

Thanks a lot. It worked fine after turning off rotamer outlier correction
and sidechain rotamer consistency in the torsion NCS options.

Subhani

On Fri, Jun 22, 2012 at 9:22 AM, Jeff Headd <jjheadd at lbl.gov> wrote:

> Hi Subhani,
>
> Are you using torsion NCS restraints? If so, the problem is the rotamer
> outlier/consistency methods. We are aware of the problem, and are working
> on a fix. In the meantime, if you turn off rotamer outlier correction and
> sidechain rotamer consistency in the torsion NCS options, that should avoid
> the problem with the current version of Phenix.
>
> Jeff
>
> On Fri, Jun 22, 2012 at 7:02 AM, Subhani Bandara <ramssb17 at gmail.com>wrote:
>
>> Hi everyone,
>>
>> I got the following error message while running refinement in mac, using
>> PHENIX-1.8-1069. This occured when refined after editing Ramachandran
>> outliers in coot, without applying Ramachandran restraints. Not sure wether
>> it has something to do with this.
>>
>> RuntimeError : Estimated memory allocation for cubicles exceeds
>> max_number_of_bytes:
>>
>>   This may be due to unreasonable parameters:
>>
>>     cubicle_edge=5
>>
>>     space_span=(3528.41,3528.41,3442.53)
>>
>>     n_cubicles=(706,706,689)
>>
>>     max_number_of_bytes=2147483648
>>
>>
>> Any suggestions!
>>
>>
>> Thanks
>>
>> Subhani
>>
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>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
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