My software notes

March 19, 2012

install procheck on MacOS 10.6

Filed under: mac,softwares and scripts — kpwu @ 10:50 pm
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Running system: MacOS X 10.6.8

First, followed by instruction of Procheck official site, download all required file. (you need to fax the license agreement first).

I use tar command to uncompress the procheck.tar.gz and aqua3.2.tar.gz.

Secondly, in procheck folder, edit the Makefile and change two lines:

F77 = gfortran # Your FORTRAN compiler
CC = gcc # Your C compiler

I have two F77 compilers, g77 and gfortran in my Mac 10.6.8 X11 environment. g77 was failed to compile the fortran macros but gfortran does very well. The gfortran package can be installed through fink. (similar solution/discussion at CCP4bb forum)

Step 3: After modifying the “Makefile”, simply type “make” at procheck folder and you will see several warnings but the required executable  macros will be generated (e.g. vplot…).

Step 4: copy the cshrc section preloaded in setup.sh to your .cshrc (or .tcsrch) file, remember to update the absolute path of your procheck (e.g. /User/admin/program/procheck). You have to update the path at “set    prodir” and “setenv   prodir“— two lines.

After updating the C shell environment (source $HOME/.cshrc), I successfully run Procheck analysis at my local iMac! Here are the example figures generated in my test run.

LigPlot on Mac OS X 10.6

Filed under: mac,softwares and scripts,web — kpwu @ 12:20 am
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A quick note of test of LigPlot on my Mac.

==background ===

If you have ever used the PDBSum service, you may notice many provided useful information including the protein-protein interaction/interface, protein-ligand or protein-DNA (or RNA) interaction/interface, Rama plot, topology and sequence.

For example (see image below), the banner of PDB file (2XUV) entry in PDBSum provides links of “protein, “ligands”, protein-protein interaction” and “clefts” for users to see the detail molecular interactions. When you click the link “ligands” in the banner or the “SO4” link in the “Contents” at left corner, you will see a image generated by LigPlot which shows both hydrophobic and hydrogen bonding interactions between ligand and protein.

=== installation on Mac =====

Following by the instruction described at LigPlot official site, I downloaded the LigPlot binary files (Linux/Unix version) to run it on my iMac (10.6.8).

After uncompressing the hbplus and ligplot file,  as instructed in the “install.doc” text file, 3 steps are essential to make ligplot run well on Mac OS 10.6:

1. user has to manually compile some files in ligplot (GCC must be installed first) :
cc -o ligplot ligplot.c -lm
cc -o hbadd hbadd.c -lm
cc -o dimer dimer.c

2. run “make” in the hbplus to compile all required C files.

3. edit either tcsh, csh or bash shell environment file as suggested in the “install.doc” file.

=== run LigPlot on Mac, an example ===

I have used HADDOCK to generate some protein-RNA docked model and LigPlot was used to see the protein-RNA contacts. Here is the example result:

 

Note: The ligplot author has another specific version called NucPlot to draw the protein-DNA or protein-RNA contacts, I didn’t try it because it just draw the molecular contacts in different style.

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