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hpatch commands and how to identify patches


Hi everyone!

I would like to determine the hpatch score for proteins to predict the affinity to lignin as described by "Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity" by Sammond et al 2014 and developed hpatch by Jacak et al.

I tried to validate the method by BSA hpatch but it is not worked (the output was 8.0 whilw should be 36).

I also don't know how to obtain the hydrophobic patch area and how to identify it in protein structure.

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Speeding up FastDesign

    <ScoreFunction name="r15" weights="ref2015.wts"/>
    <True name="full_pose"/>
    <ResfileCommandOperation name="rescmd" command="ALLAA EX 1 EX 2 EX_CUTOFF 1" residue_selector="full_pose"/>
    <FastDesign name="design" scorefxn="r15" task_operations="rescmd" repeats="3">
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trRosetta protocol Segmentation Fault

Structure prediction


So I've been trying to implement the new trRosetta protocol and I keep getting a segmentation fault error. Is there any idea what I might be doing incorrectly? The Rosetta Crash Log is below and is followed by the output logs (both raw text files are also included as attachments).

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Structure prediction

Has anyone had trouble with the Hybridize mover in RosettaScripts in the lastest weekly release Rosetta 2021.16 (Release date: Friday, April 23, 2021)? My script that works with older releases has stopped working and seg faults in Stage 4. Other movers, for example FastRelax, work.

Any help is much appreciated! Thanks.

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Filling the missing loops

Loop Modeling


I was working on a PDB structures with 3 missing loops. Two of them have more than 15 missing residues. In this case, are the loop modeling methods still applicable? If so, which algorithm should I follow? Can I ask if there is a better way to fill the loops without affecting the existing region in the PDB structure? Thank you!

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