In Windows: findstr /b /v ANISOU input.pdb > output.pdb
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Tim Gruene > Sent: Tuesday, June 11, 2013 10:40 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Fwd: [ccp4bb] pdbset > > -----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-----
