Changes between Version 6 and Version 7 of SOPs/AlphaFold


Ignore:
Timestamp:
04/23/24 06:21:59 (10 months ago)
Author:
twhitfie
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/AlphaFold

    v6 v7  
    66=== Running AlphaFold using ChimeraX ===
    77
    8 If you cannot find a predicted structure for your protein within the databases listed above, perhaps because amino acid substitutions relative to the reference sequence are present, [https://www.cgl.ucsf.edu/chimerax/ ChimeraX] is an [https://www.youtube.com/watch?v=gIbCAcMDM7E easy place to start due to its graphical user interface] and convenient visualization tools.
     8If you cannot find a predicted structure for your protein within the databases listed above, perhaps because amino acid substitutions relative to the reference sequence are present, [https://www.cgl.ucsf.edu/chimerax/ ChimeraX] is an [https://www.youtube.com/watch?v=gIbCAcMDM7E easy place to start due to its graphical user interface] and convenient visualization tools.  You will need to install ChimeraX on a desktop or laptop computer, but the AlphaFold predictions will be made using computing resources in the cloud.
    99
    10 === Running AlphaFold locally ===
     10=== Running AlphaFold using computing resources at Whitehead ===
    1111
    1212It may happen that the freely available computational resources accessed via ChimeraX are a constraint on completing your AlphaFold predictions.  In that case, you can make the predictions locally using a command like the following: