Re: [PyMOL] how can quickly make a fractional atoms into one

[Thomas H. <sp...@us...>]

On 10/11/2011 10:16 AM, Tsjerk Wassenaar wrote:
> Not really a Pymol question, is it?

well, it's the segment identifier column, so you can do with PyMOL:

set pdb_retain_ids
load input.pdb
alter all, segi=''
save output.pdb

Cheers,
   Thomas

> On linux you can use sed:
>
> sed '/^\(ATOM\|HETA\)/s/^\(.\{72\}\)..../\1    /' filein.pdb>  fileout.pdb
>
> That means:
>
> /^\(ATOM\|HETA\)/ :: Match lines starting with ATOM or with HETA, and
> on those lines execute:
> s/^\(.\{72\}\)..../\1    / :: Subsitute the first 72 characters and
> the following four by the first 72 and four spaces. '\1' refers to the
> 72 stored characters: \(.\{72\}\}
>
> Hope it helps,
>
> Tsjerk
>
>
> On Tue, Oct 11, 2011 at 9:59 AM, lina<lin...@gm...>  wrote:
>> Hi,
>>
>> I wish to change
>>
>> ATOM    822  H01 PDB     1      32.103  36.531  -0.203 -0.11  0.02      .296
>> H
>> ATOM    823  C12 PDB     1      34.140  35.147  -0.218 -0.18 -0.01      .122
>> C
>>
>> to:
>>
>> ATOM    822  H01 PDB     1      32.103  36.531  -0.203 -0.11
>> 0.02             H
>> ATOM    823  C12 PDB     1      34.140  35.147  -0.218 -0.18
>> -0.01             C
>>
>> only the last field.
>>
>> How can I quickly achieve it.
>>
>> Thanks,

-- 
Thomas Holder
MPI for Developmental Biology