[Chimera-users] Not Responding
pett at cgl.ucsf.edu
Thu Jun 30 16:05:52 PDT 2011
My first inclination would be to think that the culprit is Chimera's
ring-finding code, but the fact your input files work while your
output files don't is perplexing. I don't think I can really help
unless you send me some files to work with (one input and one output
would be good).
UCSF Computer Graphics Lab
On Jun 30, 2011, at 11:36 AM, Chad Junkermeier wrote:
> I have been having strange behavior lately with opening coordinate
> files. I am using xyz format files with up to 500 atoms. When I
> tell Chimera to open one of these files the computer sits for a
> moment and then starts reporting that Chimera is "Not Responding."
> I have tried this on three different Mac computers, one using OS X
> 10.6.7 (iMac Core i7, 8 GB Ram, ATI Radeon HD 4850) with all of the
> latest updates, one using OS X 10.6.7 (iMac Core 2 Duo, 4 GB Ram,
> NVIDIA GeForce 9400), and one 3 or 4 year old Macbook that has (4GB
> RAM, and I don't know anything else). On each of these machines I
> have tried using a variety of different versions of your code, and I
> continually find that I have the same problem. I also just
> installed Chimera on a Windows XP machine and it has similar issues.
> The xyz files are the product of relaxing a graphene sheet in
> Quantum Espresso, and then copying and pasting the final
> configuration out of the QE output file into a xyz file.
> Here are a few of the things that puzzle me. First, if I place the
> input configuration of atoms into a xyz file, Chimera will read in
> the structures without any problems. The output xyz files work in
> VMD and in iMol. I thought that it might be an issue with the xyz
> data structure and transformed it to PBD and it still wouldn't
> load. I also wondered if it was an issue of too many decimal points
> (higher precision than the input file), but after reducing the
> number of decimal points of each coordinate on all of the atoms, it
> still wouldn't work. I have looked through some of the output files
> and there doesn't appear to be any weirdness in any of the files.
> Further complicating this issue is that sometimes, after if I let it
> sit for a while, the program magically starts working.
> Again, I have no problem opening other files.
> Does anyone have any ideas on what to do to fix this problem?
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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