How to use ResQ in local?

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Davidwang
Posts: 2
Joined: Wed Oct 19, 2022 2:49 pm

How to use ResQ in local?

Post by Davidwang »

Hi,
I had eight thousand protein structures generated by using Rosetta, and I want to get B-factor from these structures.
I found ResQ can work for this, and downloaded the I-tasser and libs for B-factor predict.
However, it didn't work with the information that "LOMETS failed", how can I solve this problem.
Or if there are simple software to calculate B-factor separately, can you recommend one or two,
thanks a lot
jlspzw
Posts: 94
Joined: Tue May 04, 2021 5:04 pm

Re: How to use ResQ in local?

Post by jlspzw »

Dear user,

ResQ download and usage can be found here https://zhanggroup.org/ResQ/download/

Let me know if you followed that instruction or not?

If you follow that instruction, is that error come from 2) runResQ.pl?

Please attach all the error messages if possible.

Also, I would suggest you first make sure the I-TASSER suite and its lib are set up correctly on your computer, then run ResQ. To make sure, you can go to I-TASSER suite package, run runI-TASSER.pl in I-TASSERmod folder to check it.

Let us know the updates. Thank you.

Best
IT team
Davidwang
Posts: 2
Joined: Wed Oct 19, 2022 2:49 pm

Re: How to use ResQ in local?

Post by Davidwang »

/share/home/cau_wangsw/software/ROSETTA/ITASSER/I-TASSER5.1/ResQ/runResQ.pl
-pkgdir /share/home/cau_wangsw/software/ROSETTA/ITASSER/I-TASSER5.1
-libdir /share/home/cau_wangsw/software/ROSETTA/ITASSER/lib
-protname A.pdb
-model A.pdb
-datadir /share/home/cau_wangsw/software/ROSETTA/Loopmodels/AVRPik
-java_home /share/home/cau_wangsw/software/IPR/jdk

#lib: Bfactor CNT DEP dotProfiles MTX PDB SIG stride summary

Your setting for running ResQ is:
-pkgdir = /share/home/cau_wangsw/software/ROSETTA/ITASSER/I-TASSER5.1
-libdir = /share/home/cau_wangsw/software/ROSETTA/ITASSER/lib
-protname = A.pdb
-datadir = /share/home/cau_wangsw/software/ROSETTA/Loopmodels/AVRPik
-java_home = /share/home/cau_wangsw/software/IPR/jdk

run /share/home/cau_wangsw/software/ROSETTA/Loopmodels/AVRPik/R_A.pdb_A.pl...
Hostname: hw88
Started : Thu Oct 20 11:54:43 CST 2022

Path : /share/home/cau_wangsw/software/ROSETTA/ITASSER/I-TASSER5.1/I-TASSERmod

running LOMETS...
LOMETS failed.
Please check
ResQ done
jlspzw
Posts: 94
Joined: Tue May 04, 2021 5:04 pm

Re: How to use ResQ in local?

Post by jlspzw »

Dear user,

We doubt the I-TASSER package is not correctly set.
Can you first go to /share/home/cau_wangsw/software/ROSETTA/ITASSER/I-TASSER5.1, to check if the I-TASSER setting is correct?

You can first check the README file in I-TASSER5.1 and run the example in I-TASSER5.1 with the main program at /share/home/cau_wangsw/software/ROSETTA/ITASSER/I-TASSER5.1/I-TASSERmod/runI-TASSER.pl, then let us know if anything is incorrect with the output and errors.

Best
IT team
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