>From the previous task it's OK now
small question about pymol :)
how to prevent removing TER record after editing of the structure using
pymol
e.g I used the following command to load protein-ligand complex (where
there is TER between protein and ligand) and remove hydrogens and than save
back it to new pdb where there were no more TER records
pymol $pdb -c -q -d "remove hydrogens; save
${temp}/${filenamenoextention}_noH.pdb, ${filenamenoextention}" >
${temp}/xz.log
and smth about shell informatics:
how to scan specified string in pdb corresponded to the last line of the
ligand (which is the RES in pdb) and add after this line TER record. E.g
the basic idea:
grep -v "ATOM.*\(RES\|MOL\)" $pdb | # smth with sed > pdb_with_TER.pdb
now I only would like to know proper reg expression in my case for GREP and
command for SED
James
2014-09-24 11:06 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> some additional question about shell scripting (copied from the amber
> forum because I'd like to find as more sollutions of this problem as
> possible):
>
>
> I wounder about possibilities to define disulphide bond between any pairs
> of SG atoms of CYX residues using amber's tleap scripts in some automatic
> fashion.
>
> In my case I use tleap as part of some big script to process many
> models.pdb for further md simulation. Each of the model consist of pair of
> CYX residues (assigned by pdb2pqr) in different positions of its sequence.
> So in script I need firstly to know the number of position for each of CYX
> residues of each model and than to fill this numbers to the tleap input
> files for each model
>
> in bash for one model it will be look like:
>
> #some command to scan the sequence of model.pdb and define pair of its CYX
> residues within it as the k ans i variables
> printf "source leaprc.ff03.r1\nprotein = loadpdb model.pdb\nsetbox
> protein centers\nbond protein.${k}.SG protein.${i}.SG\nsaveamberparm
> protein protein.parm7 protein.inpcrd\nquit" > ./tleap.in
>
>
> so my task is only to find some command which will scan model and find
> positions of the CYX within its sequence which could be put to the tleap as
> two digits. It will be better to find those 2 digits using pdb as an input
> and some unix command like sed or grep to find positions
>
> I will be very thankful for any suggestions!
>
> James
>
>
>
> 2014-09-12 16:21 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>:
>
>>
>> csplit -b "%03d.pdb" test.pdbqt /^MODEL/ {0} > somelog.log
>>>
>>
>> man csplit:
>>
>> csplit -f blabla -b "%03d.pdb" test.pdbqt /^MODEL/ {1}
>>
>> But you want only the first frame anyway, so no real use for csplit...
>>
>> sed /^ENDMDL/q my_docking.pdb | grep -v "^ROOT\|^ENDROOT\|^TORSDOF
>>> 0\|^MODEL\|^REMARK" | sed -e 's/^ENDMDL/TER/g' > firstmodel.pdb
>>>
>>
>> sed -e '/^ENDMDL/{s/^.*/TER/;q;}' -e '/^\(ROOT\|ENDROOT\|TORSDOF
>> 0\|MODEL\|REMARK\)/d' my_docking.pdb > firstmodel.pdb
>>
>> ... shorter and one process running in stead of 3.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
>
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