You are here

Error using InterfaceHoles filter

5 posts / 0 new
Last post
Error using InterfaceHoles filter

I'm trying to use the InterfaceHoles filter and get the following error:

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER holes=======================
core.scoring.packing.compute_holes_score: compute_holes_surfs try: 1
sh: 1: alpha20_surf: not found

Any idea where alpha20_surf needs to be (or if it needs to be compiled?)


Here's my simple xml script to test out the filter:





        <InterfaceHoles name="holes" jump=1 threshold=200/>



        <Add filter="holes"/>


Thanks in advance.

Post Situation: 
Fri, 2017-04-14 08:55

As the documentation for InterfaceHoles points out, albeit rather cryptically, you need to set the -holes:dalphaball option to the DAlphaBall executable.  Without it, you'll get that cryptic error, where a  DAlphaBall option is being treated as a program.

You can actually find the source for DAlphaBall (or at least the version which works with Rosetta) in the Rosetta distribution, under Rosetta/main/source/external/DAlpahBall/  It's not compiled by default, so you may have to do some light editing of the Makefile for your platform, and then run `make` to build the program. If successful, a new executable file (DAlphaBall.gcc on my machine) will be generated in that directory. That's the filename (with full path) that you should pass to -holes:dalphaball 

Fri, 2017-04-14 09:21

Thanks for the quick reply!  This works now.  When I read the documentation I thought the user only needs to pass "-holes:dalphaball" without an argument.

In case other folks need to use this, DAlphaBall compiles fine under Ubuntu 16.04 (I only needed to get the libgmp3-dev package installed).

Fri, 2017-04-14 10:12

Can you please explain how you compiled it in ubuntu? or at least how to compile it through changing the Makefile?

Mon, 2017-07-24 09:55


I was just able to compile on a different workstation (Ubuntu 16.04).  No changes were necessary to the Makefile.

# install libgmp3-dev

sudo apt-get install libgmp3-dev

After this installs, compile the executable:


I get a couple warnings, but the code compiles fine.  Here's my gcc version:

gcc -v
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.4' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4)

Mon, 2017-07-24 11:06