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). --Eric 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@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@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@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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users