From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Wed Jun 11 2014 - 10:29:05 CDT
Hello Gurpreet,
That kind of string manipulation is calling for vim, awk, sed, R,
Python, Perl and many others. To do that with a single PDB file, I
would go for vim. For many files, I would use Python.
Now the important part: Have you checked the documentation of the PDB
format to make sure that residue names such as ARM93000 are accepted?
Here is the link:
http://www.wwpdb.org/documentation/format33/v3.3.html
In particular, if you go to
http://www.wwpdb.org/documentation/format33/sect9.html#ATOM
you will find that ARM93000 is too long a residue name.
Also, the way the PDB format is defined, each character is a column.
So, the 4th column is actually the letter "M" in the word "ATOM".
Summary:
The change from 1,1,1... to 1,2,3,...,93000 can be done but the
resulting PDB would be unusable.
If somebody in the list knows better, please step in and correct me.
Thank you,
Ivan
Ivan Gregoretti, PhD
Bioinformatics
On Wed, Jun 11, 2014 at 10:39 AM, Gurpreet Kaur Dhindsa
<el2275_at_wayne.edu> wrote:
> Dear All,
> I have a pdb which looks like this
> ATOM 1 CA ARM1N 1 -62.463 -17.910 -2.486 0.00 0.00 NT1 C
> ATOM 2 CA ARM1N 1 -62.463 -17.910 1.081 0.00 0.00 NT1 C
> ATOM 3 CA ARM1N 1 -62.463 -17.910 4.648 0.00 0.00 NT1 C
> ATOM 4 CA ARM1N 1 -62.463 -14.343 -9.620 0.00 0.00 NT1 C
> ATOM 5 CA ARM1N 1 -62.463 -16.127 -7.837 0.00 0.00 NT1 C
>
> I want to change the number "1" in 4th column of my pdb to 1,2,3,4,.....93000. I have 93000 number of atoms.
> Can someone please tell me how I can change it in VMD if it is possible?
> Thanks,
> Gurpreet.
>
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