Array is not properly allocated

Submitted by bobg on Tue, 2015-10-13 11:06

Forums

Magdistortion

I am trying to run Tim’s program to estimate if there is any
anisotropy in our scope and am getting an error array is not properly
allocated. I aligned with DM and created an aligned micrograph to put
into the program. Does the program require a stack of frames or is
there a problem with the mrc output from DM? Thanks.
Bob

timgrant Tue, 2015-10-13 11:14

Hi Bob,

The input is a stack of single images. The idea is that there are 10-20 images of different crystalline areas (the default settings should work with gold, but other things should also work). The program will take each of the images, extract the amplitudes and average them to hopefully end up with an average spectra that contains a ring (more or less). This ring is what is used for the estimation.

Do you just have a single image, or do you have a stack? Either way, the program shouldn't crash, so that sounds like a bug.

Let me know, and I will look into it.

Thanks.

Tim

bobg Tue, 2015-10-20 11:59

Hi Tim,
I stacked the images and tried running it again. I got the same error. Any luck finding the bug or suggestions of what I can try? Thanks.
Bob

PS I replied to this earlier last week and the post disappeared.

timgrant Tue, 2015-10-20 13:03

Hi Bob,

Is this a stack of images, with each image in the stack being an image of a different crystalline area?

At any rate, this sounds like there is a bug. Is there a way you could make the images available to me so that I can try and reproduce the error?

Thanks,

Tim

bobg Thu, 2016-01-07 09:02

Hi Tim,
Sorry I did not notice this post until now. I am not monitoring the forum. In the mean time we tried collecting the input data with leginon rather than directly with DM and that solved the problem. DM seems to output some sort of altered MRC file which can not be recognized. I also had this problem when running FINDDQE but was able to resolve it using SPIDER but not so in this case. I can send you one of the stacks if you like but for now we are OK.
Thanks,
Bob