-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Swastik Phulera,
if your res-file sports negative U-values, your model has room for improvement. You really should go back to the ins-file and make the appropriate modifications in order to get rid of negative U-values (the do not make chemical sense!). Do you use RIGU? It might overcome your problem. Negative B-values (of waters) could also mean that you placed an oxygen instead of a heavier ion. Best, Tim On 06/11/2013 11:42 AM, Swastik Phulera wrote: > 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: > > 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/ iD8DBQFRtwdfUxlJ7aRr7hoRAsy/AKCI1LfMVm9XM8HQfYacV91pRqK/3ACgtcSY LT/zS9Igbt0Q/EghhpU4LDw= =MCpu -----END PGP SIGNATURE-----
