-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Swastik Phulera,
unless you need the ANISOU cards, you can first remove them with e.g. grep -v "^ANISOU" youfile.pdb > yournewfile.pdb before running pdbset. (I hope you don't work on a Windows machine, then you would probably first find a way to install 'grep', a command common on unixoid operating systems). By the way: how did you get negative B-values into your PDB-file? Best, Tim On 06/11/2013 10:22 AM, Swastik Phulera wrote: > ---------- Forwarded message ---------- From: Swastik Phulera > <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> > > > 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>wrote: > > 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/ iD8DBQFRtuJQUxlJ7aRr7hoRAhcWAKDGPXBS3iJhzzbaYBK4GnJGjijyngCgqYZI B26VKBDFO5FQNJJQd6plsc8= =mDut -----END PGP SIGNATURE-----
