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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
> <[log in to unmask]> 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 <[log in to unmask]> Date: Tue, Jun 11, 2013
>>>> at 1:51 PM Subject: Re: [ccp4bb] pdbset To: Tim Gruene
>>>> <[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]>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
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