Question: Parallel Processing In Ucsf Chimera
1
gravatar for Harpalss
9.2 years ago by
Harpalss310
Harpalss310 wrote:

Im conducting a number of superpositions (match maker in Chimera) on large protein structures. I was wondering if these superpositions can be parallel processed? So I have a number of superpositions running at once?

protein structure • 2.0k views
ADD COMMENTlink modified 9.1 years ago by dimkal730 • written 9.2 years ago by Harpalss310

First, why Chimera? You should use the structure superposition program most appropriate for your task. Things that affect the program choice is expected structural difference between the proteins, whether they have different sequence, and whether you want to create multiple structure superposition. E.g. for remote structures choose TM-Align, for multiple structure superposition of proteins with detectable sequence similarity choose Theseus. Last, maybe this ultra-fast method fits your needs: http://theobald.brandeis.edu/qcp/

ADD REPLYlink written 9.0 years ago by Jan Kosinski1.6k
0
gravatar for User 2204
9.2 years ago by
User 22040
User 22040 wrote:

You could run multiple Chimeras at once. How you do that depends on what kind of machine you're on. You should probably ask this question on the chimera-users mailing list (http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users/index.html) for the best answer.

ADD COMMENTlink modified 16 months ago by _r_am32k • written 9.2 years ago by User 22040
0
gravatar for João Rodrigues
9.1 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

For protein superposition I would more likely use some software like Profit that is not only more likely to be faster but also easier to parallelize.

ADD COMMENTlink written 9.1 years ago by João Rodrigues2.5k
0
gravatar for dimkal
9.1 years ago by
dimkal730
United States
dimkal730 wrote:

if you're doing lots of structure superimposition, you may want to look into tools designed specially for that (ie: MAMMOTH).

ADD COMMENTlink written 9.1 years ago by dimkal730
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1616 users visited in the last hour
_