[phenixbb] phenix.find_ncs_from_density density_search.dump_ncs_density doesn't output mtz

Terwilliger, Thomas C terwilliger at lanl.gov
Wed Dec 11 14:37:25 PST 2013


Hi Francis,

No, unfortunately phenix.find_ncs_from_density doesn't know about multi-domain NCS...

All the best,
Tom T

On Dec 11, 2013, at 3:29 PM, Francis Reyes wrote:

> Thanks Tom, 
> 
> Does phenix.find_ncs_from_density cope with multi-domain NCS? 
> 
> F
> 
> On Dec 11, 2013, at 11:39 AM, Terwilliger, Thomas C <terwilliger at lanl.gov> wrote:
> 
>> Hi Francis,
>> Oh hmmm, I'm sorry! You are right. You need a nightly build for that option, as I put it in since the last official release.
>> All the best,
>> Tom T
>> 
>> On Dec 11, 2013, at 11:03 AM, Francis Reyes wrote:
>> 
>>> Hi Tom
>>> 
>>> 
>>> Phenix 1.8.4-1496 doesn't have this option for phenix.find_ncs_from_density ? 
>>> 
>>> Thnx, 
>>> $ phenix.find_ncs_from_density  find_ncs_from_density_params.eff ncs_mask_file=foo.mtz
>>> Parameters taken from: find_ncs_from_density_params.eff
>>> Sorry: 
>>> Sorry, cannot interpret the keyword: ncs_mask_file=foo.mtz
>>> 
>>> 
>>> 
>>> F
>>> 
>>> On Dec 11, 2013, at 8:33 AM, Terwilliger, Thomas C <terwilliger at lanl.gov> wrote:
>>> 
>>>> Hi Francis,
>>>> 
>>>> Try this:
>>>> 
>>>> phenix.find_ncs_from_density map_coeffs.mtz ncs_mask_file=ncs_mask.mtz
>>>> 
>>>> and look for ncs_mask.mtz
>>>> 
>>>> (dump_ncs_density instead dumps average density to temp_dir/ncs_avg_map_coeffs.mtz)
>>>> 
>>>> All the best,
>>>> Tom T
>>>> 
>>>> 
>>>> On Dec 10, 2013, at 11:50 PM, Francis Reyes wrote:
>>>> 
>>>>> I'd like to see the region of my maps that obey the NCS operators and I was hoping for separate mtz's for each region given I had set density_search.dump_ncs_density = True. However, I'm not getting any output mtzs. Any ideas?
>>>>> 
>>>>> Thanks,
>>>>> F
>>>>> 
>>>>> 
>>>>> 
>>>>> ---------------------------------------------
>>>>> Francis E. Reyes PhD
>>>>> 215 UCB
>>>>> University of Colorado at Boulder
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
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> 
> 
> ---------------------------------------------
> Francis E. Reyes PhD
> 215 UCB
> University of Colorado at Boulder
> 
> 
> 
> 
> 
> 
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