> My research assistant has downloaded the Windows executable of EDTSurf, but he is only getting 3 outputs: XX_cav.pdb, XX.ply, and XX.asa. Critically, the XX.dep output files are missing.
> When he runs $ --help:
> usage: EDTSurf -i pdbname ...
> -o outname
> -t 1-MC 2-VCMC
> -s 1-VWS 2-SAS 3-MS 4-SES
> -c 1-pure 2-atom 3-chain
> -p probe radius [0,2.0]
> -f scale factor (0,20.0]
> -h 1-in and out 2-out 3-in
> output1: outname.ply
> output2: outname.asa
> output3: outname-cav.pdb
>
> It appears that the program is not set to output the residue depth file. He is not sure how to set the program to generate these outputs. He tried all the different surface type flags (-s) and the triangulation type flag (-t) none worked.
EDTSurf:EDTSurf program is not generating the XX.dep output files as expected
Moderator: robpearc
Re: EDTSurf:EDTSurf program is not generating the XX.dep output files as expected
Thank you for reaching out regarding the issue with the EDTSurf outputs. I understand the importance of resolving this matter promptly for your research assistant.
After reviewing the provided information, it seems that the EDTSurf program is not generating the XX.dep output files as expected. Based on the usage instructions you shared, it appears that your research assistant has tried various surface type flags (-s) and triangulation type flags (-t) without success.
To address this issue, I recommend using the following command: ./EDTSurf.exe -i **.pdb -s 0
This command should resolve the problem and ensure that the XX.dep output files are generated successfully. I'm very sorry that the output description caused you misleading.
After reviewing the provided information, it seems that the EDTSurf program is not generating the XX.dep output files as expected. Based on the usage instructions you shared, it appears that your research assistant has tried various surface type flags (-s) and triangulation type flags (-t) without success.
To address this issue, I recommend using the following command: ./EDTSurf.exe -i **.pdb -s 0
This command should resolve the problem and ensure that the XX.dep output files are generated successfully. I'm very sorry that the output description caused you misleading.
Re: EDTSurf:EDTSurf program is not generating the XX.dep output files as expected
We have discovered that the precompiled version of EDTSurf_mac available on the website may be outdated and not fully compatible with the current macOS version. To address this issue, we recommend downloading the source code directly from the EDTSurf website (https://zhanggroup.org/EDTSurf/) and compiling it on your MAC.
You can follow these steps to compile the source code:
Download the source code package from the provided link.
Extract the contents of the package to a directory on your Mac.
Open Terminal and navigate to the directory containing the extracted source code.
Run the appropriate build commands (e.g., make) to compile the source code and generate the new EDTSurf executable.
Once the compilation is complete, you can use the new EDTSurf executable along with the -s 0 flag to generate the XX.dep files as expected.
We believe that using the newly compiled executable should resolve the issue you encountered on Mac.
You can follow these steps to compile the source code:
Download the source code package from the provided link.
Extract the contents of the package to a directory on your Mac.
Open Terminal and navigate to the directory containing the extracted source code.
Run the appropriate build commands (e.g., make) to compile the source code and generate the new EDTSurf executable.
Once the compilation is complete, you can use the new EDTSurf executable along with the -s 0 flag to generate the XX.dep files as expected.
We believe that using the newly compiled executable should resolve the issue you encountered on Mac.
Re: EDTSurf:EDTSurf program is not generating the XX.dep output files as expected
We have update EDTSurf_mac executable in the EDTSurf website (https://zhanggroup.org/EDTSurf/).