[Chimera-users] Not Responding

[Eric Pettersen]

Hi Chad,
	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).

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Jun 30, 2011, at 11:36 AM, Chad Junkermeier wrote:

> Hello,
> 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?
>
>
> Chad
>
>
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