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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* <[log in to unmask] > <mailto:[log in to unmask]>> > Date: Tue, Jun 11, 2013 at 1:51 PM > Subject: Re: [ccp4bb] pdbset > To: Tim Gruene <[log in to unmask] <mailto:[log in to unmask]>> > > > 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 <[log in to unmask] > <mailto:[log in to unmask]>> 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 > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFRtsaJUxlJ7aRr7hoRAiAsAKCuDDip6GFczecze/Y18+YaD4+SqACdGnSU > fG1/zzDml0ynkX8uOBN7S+o= > =2I5+ > -----END PGP SIGNATURE----- > > > > > -- > -- > 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 > > > > -- > -- > 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 F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494