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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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