[chimerax-users] Could you please inform the best advice to solve a structure via colabfold when GPU is an issue? I tried some routes already.

[Josh Gutierrez]

Hello,

I recently submitted a job through ChimeriaX and used the "prediction" task
for it to be solved via Alphafold2-- the sequence is about 1300 amino acids
in length. However, the protein could not be solved by alphafold2 and the
colabfold reports the GPU consumption is too high for the structure to be
solved. To resolve the problem, I tried breaking the sequence into two to
solve this expected bimodal protein individually (into two separate
structural parts) and even in combination purchased "compute units" for
more memory and storage to do this, but the structure can't be solved
without high predicted error.

Please let me know what you think may  resolve this issue. Currently, I am
working with an external professor who may be able to connect me with a
collaborator on this issue at UCSF if there is a cluster or core we can use
to expedite the process to solve this structure I am addressing. Please let
me know your thoughts at your earliest convenience. Please also let me know
if you need any more information!

Many thanks,
Josh Gutierrez
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20230414/e660603d/attachment.html>