Re: Writing pdb file.. easier way?

From: griadi_at_utalca.cl
Date: Tue Nov 23 2004 - 12:44:03 CST

Hey Uday,

I use Swisspdb to do those residue number conversions. You can download it
here:
http://us.expasy.org/spdbv/text/download.htm

Cheers!
Gonzalo.

Mensaje citado por Jérôme Hénin <jerome.henin_at_uhp-nancy.fr>:

> Hi Uday,
>
> I am sure there is a nice VMD way of doing this, but here is the quick and
> dirty (not so dirty, actually) AWK way:
>
> -------
> #!/bin/awk -f
> $1=="ATOM" {
> printf("%s%4i%s\n", substr($0, 1, 22), substr($0, 23, 4) + 100,
> substr($0, 27, 60))
> }
> $1!="ATOM" {
> print
> }
> -------
>
> Of course, you may type it all in a single command line if yo like it better
>
> than an executable script.
>
> Jerome
>
> Le jeudi 18 Novembre 2004 15:58, Uday Chippada a écrit :
> > I have another simple question. If I have a pdb file of the sort shown
> > below, and I have to change the residue numbers from say 301 to 401, 302
> to
> > 402 and so on, is there a simple way to do it using VMD or any text
> > commands? I have tried cat filename.pdb | awk '{print $1 $2 $3 $4 $5
> $6+100
> > ... }' > newfile.pdb
> >
> > But this new file is not being read by VMD, must be the format error (the
> > spacings between different columns in the line). Is there a way in which I
> > can get a nice spacing, like how we get when we use the "writepdb" ?
> >
> > I need to change the residue numbers as I was trying to merge different
> > files with same resid numbers, but different coordinates.
> >
> > Thanx
> >
> > Uday
> >
> > ATOM 1 N PRO A 301 -7.354 25.615 61.612 1.00 26.07
> >
> > ATOM 2 CA PRO A 301 -6.259 25.170 60.715 1.00 25.38
> >
> > ATOM 3 C PRO A 301 -6.330 25.908 59.378 1.00 24.47
> >
> > ATOM 4 O PRO A 301 -7.381 26.437 59.009 1.00 24.48
> >
> > ATOM 5 CB PRO A 301 -6.398 23.670 60.496 1.00 25.97
> >
> > ATOM 6 CG PRO A 301 -7.798 23.365 61.012 1.00 26.29
> >
> > ATOM 7 CD PRO A 301 -8.264 24.501 61.935 1.00 26.63
> >
> > ATOM 8 N HYP A 302 -5.206 25.961 58.640 1.00 23.36
> >
> > ATOM 9 CA HYP A 302 -5.175 26.645 57.342 1.00 21.80
>
>

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