Re: Writing pdb file.. easier way?

From: LEWYN LI (ll2150_at_columbia.edu)
Date: Thu Nov 18 2004 - 16:29:36 CST

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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