[phenixbb] atom selection in phenix.pdbtools

Pavel Afonine pafonine at lbl.gov
Wed Sep 1 19:02:59 PDT 2010


  Cool! That's for few of those who can solve a structure with a pencil 
and a sheet of paper -:) Sometimes I wish I'm 10 years older so I'm not 
spoiled with the technology and understand these "hieroglyphs".

Thanks Ed, it's always good to know a backdoor!

Pavel.

On 9/1/10 6:49 PM, Ed Pozharski wrote:
> You can just do this
>
> grep 'A 400' structure.pdb | grep -v  REMARK | cut -c 61-66 | awk '{s+=
> $1} END {print s/NR}'
>
>
>
> On Wed, 2010-09-01 at 15:02 -0700, Michael Hothorn wrote:
>> Hi,
>>
>> I want to calculate the mean b-value for all atoms of a specific ligand
>> in my structure. I tried:
>>
>>   phenix.pdbtools --show-adp-statistic model.pdb keep="chain A and
>> residue 400"
>>
>> , but it still prints out all b-values including solvent etc.
>>
>> any ideas?
>>
>> thanks
>> Michael




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