Error using InterfaceHoles filter

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    • April 14, 2017 at 3:55 pm #2633
      Anonymous

        Hi,

        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:

        <ROSETTASCRIPTS>

            <SCOREFXNS>

            </SCOREFXNS>

            <RESIDUE_SELECTORS>

            </RESIDUE_SELECTORS>

            <TASKOPERATIONS>

            </TASKOPERATIONS>

            <FILTERS>

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

            </FILTERS>

            <MOVERS>

            </MOVERS>

            <APPLY_TO_POSE>

            </APPLY_TO_POSE>

            <PROTOCOLS>

                <Add filter=”holes”/>

            </PROTOCOLS>

        </ROSETTASCRIPTS>

        Thanks in advance.

      • April 14, 2017 at 4:21 pm #12277
        Anonymous

          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 

        • April 14, 2017 at 4:21 pm #12798
          Anonymous

            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 

          • April 14, 2017 at 4:21 pm #13319
            Anonymous

              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 

            • July 24, 2017 at 4:55 pm #13632
              Anonymous

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

                • July 24, 2017 at 6:06 pm #13633
                  Anonymous

                    Hi, 

                    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:

                    make

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

                    gcc -v

                    Using built-in specs.

                    COLLECT_GCC=gcc

                    COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper

                    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)

                • April 14, 2017 at 5:12 pm #12279
                  Anonymous

                    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).

                  • April 14, 2017 at 5:12 pm #12800
                    Anonymous

                      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).

                    • April 14, 2017 at 5:12 pm #13321
                      Anonymous

                        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).

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