[Chimera-users] dock-prep problem with Zn and K ions

Eric Pettersen pett at cgl.ucsf.edu
Mon Oct 8 15:34:19 PDT 2007

Hi Joe,
	If you care about the protonation of the SHH ligand in that  
structure then I would actually recommend you use one of the new test  
builds (follow the "Test Builds" link off the Chimera home page).   
There have been improvements since the 1.2422 release in protonating  
atoms involved in coordination complexes, and in protonating ring  
nitrogens in non-standard residues (though the latter isn't directly  
relevant in your case).


On Oct 8, 2007, at 12:17 PM, zzj wrote:

> Hi Eric,
> Sorry for the mess. The old Chimera version is 1.2259.
> I just downloaded the latest version (1.2422). It works perfectly fine
> the same PDB. Guess I'll stick to this version.
> thanks a lot.
> -Joe
> On 10/8/07, zzj <zzjsail at gmail.com> wrote:
>> Hi Eric,
>> thanks for your reply. I am using PDB 2PQO. The Chimera version is
>> beta version 1 build  2259 2006/07/11
>> platform: darwin
>> windowing system: aqua
>> I am working on a Mac OS X 10.4.10 (G5). It seems Chimera works fine
>> other than the problem I mentioned.
>> -Joe
>> On 10/8/07, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>>> I can run Dock Prep on a PDB file containing zinc (1zip) without  
>>> the problem
>>> you're getting.  Can you tell me what PDB you're using, and what  
>>> version of
>>> Chimera?
>>> --Eric
>>>                         Eric Pettersen
>>>                         UCSF Computer Graphics Lab
>>>                         pett at cgl.ucsf.edu
>>>                         http://www.cgl.ucsf.edu
>>> On Oct 8, 2007, at 10:54 AM, zzj wrote:
>>> Hi there,
>>> I am preparing dock6 files in Chimera using the Dockprep option. The
>>> Zn and K ions in the PDB files are giving me problems at the  
>>> point of
>>> adding hydrogen. Everthing works fine if I remove these ion atoms.
>>> Here is the Chimera Error message:
>>> AttributeError: addHinfoDialog instance has no attribute  
>>> "cancerlCB".
>>> I can select and highlight these ions without problem. I tried to  
>>> give
>>> different names for the ions. Nothing worked.
>>> Any suggestion is highly appreciated!
>>> -Joe
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
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