Re: Writing pdb file.. easier way?

From: Uday Chippada (chippada_at_eden.rutgers.edu)
Date: Thu Nov 18 2004 - 17:19:14 CST

Oh thanx Lewyn, I tried out the way you said and it worked. Thanx to you
Neema as well, though I havent tried your code, am sure it should work as
well.

Uday
----- Original Message -----
From: "LEWYN LI" <ll2150_at_columbia.edu>
To: "Uday Chippada" <chippada_at_eden.rutgers.edu>
Cc: "vmd-l digest" <owner-vmd-l_at_ks.uiuc.edu>; <namd-l_at_ks.uiuc.edu>
Sent: Thursday, November 18, 2004 5:29 PM
Subject: Re: namd-l: Writing pdb file.. easier way?

> Uday,
>
> Just a suggestion: in your awk script, try using printf instead of
> print, because with printf, you can specify the spacing with something
> like %3d or %.5f. For details, check out:
>
> http://www.cplusplus.com/ref/cstdio/printf.html
>
> You should be able to get the spacing you want. Good luck!
>
>
> LEWYN
>
>
> On Thu, 18 Nov 2004, Uday Chippada wrote:
>
> > 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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