Dear Tim,Fred Negative B factors and occupancies higher than one came in from shelxl, Also getting rid of Ansiou at first would lead me to an additional step of placing them in their right place later on (is there a short cut that I may take).
On Tue, Jun 11, 2013 at 2:09 PM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote: > -----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----- > -- -- 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
