j3xugit / raptorx-3dmodeling Goto Github PK

Hi,
RaptorX is a great tool. But RaptorX-3DModeling can only predict protein structure. May I ask when you will release an all-in-one standalone version to predict ligand binding site and do molecular docking?
Thank you very much!

Hi RaptorX team,

Thank you for providing such a great tool. I have a naive question but have not found an answer after walking through the website.

I wonder what is the difference between the download page of the RaptorX website and this GitHub Repository?

Thank you for your time!

Hi,

I was just wondering if there are any updates regarding the release of the software version for python3 and tensorflow?

Best regards

Hi everyone!

I am trying to run the code for the example 1pazA.fasta and I have verified that the UniRef30 database is in the correct path on the file raptorx-external.sh (as suggested on issue #6 )

export HHDB=/home/lab/RaptorX-3DModeling/hh-suite-master/databases/UniRef30_2020_03

However, I keep getting the Error as follows:

(RaptorX) myname@xxxx:~/RaptorX-3DModeling$ Server/RaptorXFolder.sh -o example/ -g -1 -m 8 -r 1 example/1pazA.fasta
ERROR: invalid or damaged sequence database to be searched by hhblits: /home/lab/RaptorX-3DModeling/hh-suite-master/databases/UniRef30_2020_03
ERROR: failed to run /home/lab/RaptorX-3DModeling/BuildFeatures/BuildMSAs.sh -d example/ -m 8 example/1pazA.fasta
ERROR: failed to run /home/lab/RaptorX-3DModeling/BuildFeatures/BuildFeatures.sh -o example/ -g -1 -m 8 -r 4 example/1pazA.fasta

Can I get some help please?

~Nat

ERROR: invalid or damaged sequence database to be searched by hhblits: /home/rpearson/Structure_Prediction_Tools/RaptorX-3DModeling/UniRef30_2020_03_hhsuite
ERROR: failed to run /home/rpearson/Structure_Prediction_Tools/RaptorX-3DModeling/BuildFeatures/BuildMSAs.sh -d ./ -m 8 ./rcsb_pdb_3NV8.fasta
ERROR: failed to run /home/rpearson/Structure_Prediction_Tools/RaptorX-3DModeling/BuildFeatures//BuildFeatures.sh -o ./ -g 1 -m 8 -r 4 ./rcsb_pdb_3NV8.fasta

Can anyone help me troubleshoot this issue? All help will be appreciated.

-Rich

Hi RaptorX team,

I'm tring to predict pair relation, but keep getting this error. The error mainly about narrowing conversion of in theano pkg.

DL4DistancePrediction4/Scripts/PredictPairRelation4OneInput.sh -d ./Test_Dist ./Test_Feat/1pazA.inputFeatures.pkl

The cmd output is too long, there are some screenshots and the detailed out-file.

Full cmd output
xsh5A07.tmp.txt

Thank you very much!

ERROR: invalid or damaged sequence database to be searched by hhblits: /data/HHDB

And the content of /data/HHDB is as follows:

(base) myname@xxxxxxxx:/data/HHDB$ ls -l -h
total 173G
-rw------- 1 528745 9100  379 5月  26  2020 UniRef30_2020_03.md5sums
-rw------- 1 528745 9100 133G 5月  26  2020 UniRef30_2020_03_a3m.ffdata
-rw------- 1 528745 9100 644M 5月  26  2020 UniRef30_2020_03_a3m.ffindex
-rw------- 1 528745 9100 5.8G 5月  26  2020 UniRef30_2020_03_cs219.ffdata
-rw------- 1 528745 9100 581M 5月  26  2020 UniRef30_2020_03_cs219.ffindex
-rw------- 1 528745 9100  33G 5月  26  2020 UniRef30_2020_03_hhm.ffdata
-rw------- 1 528745 9100  19M 5月  26  2020 UniRef30_2020_03_hhm.ffindex

Any help?
Thanks!

I run the example mention in README that use the 1pazA.a3m file to predict distance. However, when I run the command, there are some errors.

DL4DistancePrediction4/Scripts/PredictPairRelation4OneInput.sh -d ./Test_Dist ./Test_Feat/1pazA.inputFeatures.pkl

The error indicate that No model file. But I find that there indeed not exist the file in this project.

1

Hi!

I am confused about how your code calculates Meff in the a3m format when 'gaps aligned to inserts' are omitted. Specifically, it appears that the code treats matches (uppercase characters) and inserts (lowercase characters) in the same manner, and this results in a higher Meff value for the file.

To illustrate the issue, consider the following example using two sequences in the a3m format:

Sequence 1: HCTTKFCDYKAAGAEEYAQQEVVKRSYGKAFKLSISALFVTPKTAGAQVV
Sequence 2: HCTTKFCDYgKAAGAEEYAQQEVVKRSYGKAFKLSISALFVTPKTAGAQVV

In position 10 of the second sequence, there is a lowercase 'g'. Not adding a 'gap aligned to insert' in the corresponding position of the first sequence causes all subsequent residues to shift to the right and this results in considering these shifted residues as dissimilar, which are in fact the same. As a result, the number of dissimilarities increases, leading to an inflated Meff value for the MSA file.

Could you kindly explain the rationale behind this?

Hi there,

Thanks for publishing this great work. I have downloaded the models and am able to run them sucessfully.

What are these 3 numbers shown up after writing all the relaxed models?

Beside, how can one access the quality of the models?

Thanks again.