What about getting rid of the ANISOU records before processing the pdb
file, with
grep -v ANISOU input.pdb > output.pdb
?
If a program complains about ANISOU records then you use the isotropic
approximation...
That's what I would do as a quick and dirty fix.
Fred.
On 11/06/13 10:22, Swastik Phulera wrote:
---------- Forwarded message ----------
From: *Swastik Phulera* <swastik.phul...@gmail.com
<mailto:swastik.phul...@gmail.com>>
Date: Tue, Jun 11, 2013 at 1:51 PM
Subject: Re: [ccp4bb] pdbset
To: Tim Gruene <t...@shelx.uni-ac.gwdg.de <mailto:t...@shelx.uni-ac.gwdg.de>>
Dear Tim, Miguel
Thanks for your suggestions, the program does work now, but it seems
that it cant handle AnsioU s . It gives an error:
PDBSET: *** AnisoU present: cannot reset B ***
Is there any other program which would set minimum bfactors for me.
Also I am looking for a program that would set the maximum occupancy
to a desired value (It seems that pdbset can only play with the
minimum values)..
On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene <t...@shelx.uni-ac.gwdg.de
<mailto:t...@shelx.uni-ac.gwdg.de>> wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Dear Swastik Phulera,
after the word 'output.pdb' you must first hit the Enter-key which
takes you into the program pdbset.
Then you type
B_reset Minimum 0
END
and the program runs.
If you wish to do it without interaction, e.g. in a script, you can
use the shell construct '<<':
pdbset XYZIN input.pdb XYZOUT output.pdb << eof
B_reset MINIMUM 0
eof
Best,
Tim
On 06/11/2013 08:15 AM, Swastik Phulera wrote:
> Dear All, I am trying to use pdbset from the terminal and am
> constantly getting an error:
>
> [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb
> B_reset MINIMUM 0
>
>>>>>>> CCP4 library signal ccp4_general:Use: <logical name>
>>>>>>> <file name>
> (Error) raised in ccp4fyp <<<<<< pdbset: Use: <logical name> <file
> name> pdbset: Use: <logical name> <file name> Times: User:
> 0.0s System: 0.0s Elapsed: 0:00
>
> Does any one have any idea what's wrong here?
>
>
> Swastik Phulera
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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स्वस्तिक फुलेरा
वरिष्ठ अनुसंधान कर्ता
संरचनात्मक जीवविज्ञान प्रयोगशाला
डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र
हैदराबाद, ५००, ००१
और
राष्ट्रीय कोशिका विज्ञान केंद्र
पुणे विश्वविद्यालय परिसर,
गणेशखिंड
पुना, ४११,००७
--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
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