>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
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
> 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" | se
Hi Tsjerk,
many thanks for the suggestions
in my case
csplit -b "%03d.pdb" test.pdbqt /^MODEL/ {0} > somelog.log
is not good because in always produces 000.pdb which is the empty file.
Also I dont know why but all files also consist of the xx prefix (e.g
xx000.pdb xx005.pdb etc).
so in my case be
Thank you very much!
James
2014-09-12 12:36 GMT+02:00 Marko Hyvonen :
> On 12/09/2014 11:26, James Starlight wrote:
>
>> grep -v "^ROOT\|^ENDROOT\|^TORSDOF 0\^MODEL\^REMARK"|
>>
>
> I think you are missing few "|" in there:
>
> grep -v "^ROOT\|^ENDROOT\|^TORSDOF 0\|^MODEL\|^REMARK"
>
> and depen
Hi Marko,
in my case
this (long ) is works fine
gleb@gpu2:~/Documents/script/docking/Complex/OR1A1_MULTI> cat receptor.pdb
xx001.pdb | grep -v '^ROOT'| grep -v '^ENDROOT' | grep -v '^TORSDOF 0' |
grep -v '^MODEL' | grep -v '^REMARK' | sed -e 's/^ENDMDL/TER/g' >
complex.pdb
but in the below c
Hi James,
How about
egrep -v "MODEL 1|ROOT|ATOMS|ENDROOT|TORSDOF" myoriginalfile | sed
's/ENDMDL/TER/' > mynewfile
-v in egrep is to reverse the selection so you get all lines except that
ones in the expression. Without that you _only_ "grep" the lines with
those expressions.
(egrep might be
Hi James,
This is more text-file processing than it is bioinformatics. The trick is
to understand the problem, dissect it, and fit it to your toolbox on Linux.
That's actually much of bioinformatics :)
The first thing to understand is what data you have and what data you need
to have in the end.
Hi Tsjerk,
thank you very much for help.
this is a little bioinformatics question so probably it's better to ask it
here some expert of this topic like you :)
because in my case I need to further proceed each split model model (e,g
delete some lines or make changing) piping with some commands
e
Hi James,
These are the sort of questions that'll be answered elsewhere. Most notably
on stackoverflow:
http://stackoverflow.com/questions/18364411/using-regex-to-tell-csplit-where-to-split-the-file
csplit -b "%04d.pdb" file.pdb /^MODEL/ {*}
Cheers,
Tsjerk
On Fri, Sep 12, 2014 at 11:25 AM, Ja
Hi,
some new question.
I need to some combination of shell utilities to split multi_model.pdb on
several pdbs as well as separate command to seek multi_model.pdb and to
save only this model as the separare model1.pdb. I've tried to do it using
grep
grep '^MODEL 1' my_docking.pdb > model1.pdb
bu
Thanks you very much!
James
2014-09-05 20:18 GMT+02:00 Folmer Fredslund :
> Hi
>
> Small correction to Gianlucas suggestion
>
> ">" will direct the output to a file, overwriting the contents
> ">>" will direct the output to a file, appending the contents
>
> Venlig hilsen
> Folmer Fredslund
> De
Hi
Small correction to Gianlucas suggestion
">" will direct the output to a file, overwriting the contents
">>" will direct the output to a file, appending the contents
Venlig hilsen
Folmer Fredslund
Den 05/09/2014 19.16 skrev "Gianluca Santoni" :
> Don't even need cat
> simply do
>
> grep PPC
Don't even need cat
simply do
grep PPC ref.pdb > tar_i.pdb
redirecting std out with > appends it directly to the file (after the
last line)
Cheers
On 9/5/14 6:48 PM, James Starlight wrote:
> Dear Pymol users!
>
> I've decided to open new topic focused on the implementation of the
> common shel
Dear Pymol users!
I've decided to open new topic focused on the implementation of the common
shell utilities like grep awk and sed for the structural bioinformatics
tasks like processing and editing of the large sets of pdbs.
In my current task I need to copy all lipids from one pdb (called it re
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