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.

October 19, 2011

Bruker’s Topspin running on Mac

Filed under: mac,softwares and scripts — kpwu @ 2:21 pm
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Balance the report as I just made a post for Agilent’s VnmrJ. 🙂

I found from a web blog article that introduces the news–Bruker’s Topspin 3.1 for Mac.

Bruker’s brief introduction of Topspin for Mac machine includes features:
(note on 10/29/2012, the introduction seems gone at Bruker’s website)

  • Mac OS X platform for TopSpin processing
  • Inspire a new generation of NMR users, experts and students alike
  • Entirely programmed in the native Apple Mac OS X environmentData analysis, processing and simulation features for efficient small molecule and structural biology research
  • Ideal data processing and analysis aid for NMR training

Snapshots of Topspin running on Mac linked to Bruker’s example images show at here:

(note on 10/29/2012 the image was removed from the blog)

According to Bruker’s purchase link, the price is $99 of academic license for one Mac machine. The computer MAC address code must be provided meaning one license is only available for one Mac machine!!

The current version (Oct of 2011) Topspin for Mac required “Core 2 Duo” type CPU and OS 10.6 (snow leopard and later). My old macbook pro with “core duo” is not available this time. Sad. I can only try to install it on my iMac.

Maybe I should email Bruker to request something like 30-60 days free trial and make some blog articles for “Bruker Topspin on Mac” as an exchange.

April 18, 2011

[software] PDB file editor

Filed under: mac,softwares and scripts,web — kpwu @ 9:06 pm
Tags: ,

Bioinformatics.org” hosts a nice GUI-based PDB file editor. The program is written in Java and can run on MS-Win, Linux and Mac OS. Some snapshopts are showing here. I think this is a very friendly program for users who don’t know how to use shell script to change/reset  PDB parameters (e.g. chain ID, beginning number of first residue/atom, remove of heavy atom/water..etc..)

========Program information======

Protein Data Bank (PDB) file editor: web address (http://www.bioinformatics.org/pdbeditor/wiki/Main/HomePage)

=============================

Snapshot 1: target protein coordinate is loaded.

Snapshot 2: the editor window, I reset the beginning residue at 30, and the new ChaiInID is “C”

snapshot 3: the result of new coordinate

February 7, 2011

run CcpNmr Analysis on Mac

Filed under: mac,softwares and scripts — kpwu @ 4:23 pm
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For Mac users, Fink provides an easy way to install “CcpNmr Analysis” and the dependent packages. Once you installed Fink, simply type ‘fink install ccpnmr-py26″ to get all required packaged installed for Mac OS. If you prefer using Python 2.7, then type “fink install ccpnmr-py27” to install it. I am currently running the python 2.6 version on snow leopard (10.6.4) and do not get problems open 2D spectra (sparky format). I haven’t tried 3D spectra and strip window yet.

The official site of CcpNmr Analysis is hosted by the CCPN.

There is a CCPNMR biomolecular NMR wiki  google site, nice documents can be found.

Here is the snapshot of the “analysis” (in CcpNmr, the main program is called “analysis”).

updated: April 19, 2011.

December 27, 2010

Test reports of CS-Rosetta (3.1)

Filed under: mac,softwares and scripts,xplor/xplor-nih/cns — kpwu @ 1:08 pm
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On Dec 23rd, I successfully install Rosetta 3.1 and CS-Rosetta on my iMac and run the test using GB3 protein which was provided within the CS-Rosetta.

Here are the rough steps I used to get a simulated GB3 protein.

  1. run “runCSRjob3.com” as instructed in the online manual
  2. The RunRosetta3.com has to be modified first to perform ab initio simulation by Rosetta3.
    (basically, just replace all double colon “::” in the RuRosetta3.com by single colon “:”).
  3. After ~70 hours simulation using a single CPU (3.06 GHz) on my iMac, I got the simulation done.
  4. As instructed by CS-Rosetta, one has to generate a “silent output” (the extract_lowscore_decoys.py).
  5. Before running “runCSrescore3.com”, you have to edit 2 files:
    1. go to the CS-Rosetta folder, in the “com” subfolder,edit “extract_pdb3.com”, make sure no double colons are in the script same as step 3.
    2. edit runCSrescore3.com,:
    at line 28, it was “mkdir output -p” and the new one should be “mkdir -p output”,
    at line 101, it was “rm ./pred/………  -f” and the new one should be “rm -f ./pred…….”.
    Then you can run “runCSrescore3.com” and no error/warming messages will be shown.

I don’t give the program the defined seg.txt in this test.

The error message at step 5.2 look like the following lines:

==================

userssxx:rosetta>runCSrescore3.com new_silent.out
./output directory generated
mkdir: output: File exists
mkdir: -p: File exists

extracting PDB coodinates…

generate decoys raw score table file : ./output/name.rawscore.txt
decoy with the lowest energy score: S_j001_00000289
calculate rmsd to the lowest raw score decoy ( S_j001_00000289 ) and generate file : ./output/rms2LowRawScore.txt
generate rms_toLowestRawscoreModel verus score table file : ./output/name.rms.rawscore.txt
labadmin:rosetta>runCSrescore3.com new_silent.out gb3.tab
./output directory generated
mkdir: output: File exists
mkdir: -p: File exists

extracting PDB coodinates…

generate decoys raw score table file : ./output/name.rawscore.txt
rescoring decoys using sparta calculated chemical shifts…
(input chemical shift shift gb3.tab )
calculating chemical shift score for decoy S_j001_00000001
rm: -f: No such file or directory
calculating chemical shift score for decoy S_j001_00000002
rm: -f: No such file or directory
calculating chemical shift score for decoy S_j001_00000003
rm: -f: No such file or directory

===============================================================

Now, I am waiting for the back CS-prediction by Sparta and getting the scores. But I check several simulated PDB coordinates of GB3 protein, the structures are quite similar with the published one. Here is a random one.

After the complete of back CS prediction by sparta, the script RunCSrescore3.com is supposed to collect all information and generate few text file which contains the CS_chi2, rms and other information. I don’t know why the script was looking for S_j001_0001000.pdb (because I don’t have it, only 0-999.pdb), so the “pdbrms doesn’t work properly. Therefore name.rms.rescore.txt” does not have the complete information (should have 3 columns).

I did the following steps to get the complete information. All the following commands are extracted from the runCSrescore3.com

  1. set best_model = `cat name.rescore.txt | sort -g -k4 | head -n1 | awk ‘{print $1}’`
  2. pdbrms $best_model.pdb S*.pdb | awk ‘{print $2,$1}’ | sort -g > rms2LowReScore.txt
    if you have seg.txt, then the commands are:
    set seg = `cat ../seg.txt`
    pdbrms $best_model.pdb S*.pdb -seg $seg | awk ‘{print $2,$1}’ | sort -g > rms2LowReScore.txt
  3. paste name.rescore.txt rms2LowReScore.txt | awk ‘{ print $1,$6,$4 }’ > name.rms.rescore.txt

The 1000 simulated GB3 structures seem to have trend of convergence (see the figure below). If more structures as suggested by the CS-rosetta manual (e.g. 10,000 structures), the convergence should be clear.

The 20 lowest Calpha_RMSD structures (left) and 20 lowest energy structures are superimposed by the NMR plugin in pymol which RMSD of backbone atoms (residues 1-56) are 0.6  and 0.68 angstrong, respectively.

December 24, 2010

Install Xplor-NIH 2.26 on new iMac (10.6)

Filed under: mac,softwares and scripts,xplor/xplor-nih/cns — kpwu @ 9:52 am
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A short note for installation of xplor-nih 2.26 on iMac.

Few months ago, I downloaded XPLOR-NIH 2.26 for Mac OS and installed it on my new iMac (core i3, 3.06 GHz). The default configuration script does not include “Intel Core i3”  in the processor list (at xplor-nih-xxx/arch/getDarwinCPU).

The solution to make the configuration is to edit “getDarwinCPU” script. I replaced i5 by i3 at line 21 and keep everything else unchaged.  The configuration script works and an extensive test were performed, no interruption occurred.

Second note on 2/5/2011.
For version of Xplor-NIH 2.27, same edition has to be done to make it run well on my iMac. Some Mac users may have the same problem.
 

December 23, 2010

Install Rosetta-3.1 and CS-Rosetta on Mac OS 10.6

Filed under: mac,softwares and scripts — kpwu @ 7:27 pm
Tags: , , ,

A note of my installation in the last 3 days.

Machine: iMac 3.06 GHz, core i3, 4 GB Ram , OS 10.6.4

Part A –Rosetta 3.1

First download Rosetta 3.1, all the bundle stuff.
–uncompress the bundle file, and keep uncompressing all “.tgz” files
Then download corrections for rosetta_source at here: http://zinc.ucsf.edu/~colin/snow_leopard_tools.tar.gz
(see this discussion topic at Rosetta forum : node 1705)
–go to rosetta_source, uncompress the snow_leopard_tool.tar.gz and the uncompressed files will automatically overwrite the files.

— use “scons” to compile and install by command: “scons bin mode=release”

The compilation takes approximately 1 hour.

NOTE: For Mac users, you can install scons by using Fink.

Second, you need g77 to compile the rosetta_fragments, but even using the unstable packages provided in fink, the x86_64 version of g77 for  OS 10.6 is not available. I went to “high performance computing for mac os X”  to download g77-3.4 which is a binary file already. No need to compile it by yourself.
(I tried gfortran, a lot of errors occurred, but g77 does good job).

After getting g77 works, go to resetta_fragments/nnmake and type make to have pNNMAKE.gnu compiled. This is required for CS-Rosetta,too.

Part B–CS-Rosetta

First, download the all required compressed file at CS-Rosetta official site.
–chmod 711 install.com if this is not executable.
— run ./install.com and the script will ask you to provide the full path of your rosetta-3.1 (not the path of rosetta_source).

You should see error messages that the install script cannot find some Rosetta executable files and my solution is to make soft links at “rosetta_source/bin”

Do this soft link before installing CS-rosetta.

ln -s AbinitioRelax.macosgccrelease AbinitioRelax.linuxgccrelease
ln -s extract_pdbs.macosgccrelease extract_pdbs.linuxgccrelease

— After installation, you should see something like “no errors found” and put the environmental setup in your csh or tcsh and source/update the shell.

To test the CS-Rosetta, I directly go to examples/input, type: runCSRjob3.com gb3.tab and I got:

===============

usersxxx:input>runCSRjob3.com gb3
gb3.pdb gb3.tab
lusersxxx:input>runCSRjob3.com gb3.tab
pre-checking input chemcial shift data …
*** Shift outlier: 14 G C Secondary Shift: -3.765 Limit: -3.725
*** Shift outlier: 15 E HA Secondary Shift: 1.313 Limit: 1.047
*** Shift outlier: 17 T HA Secondary Shift: 1.498 Limit: 1.047
*** Shift outlier: 19 K HA Secondary Shift: 1.070 Limit: 1.047
*** Shift outlier: 25 T CA Secondary Shift: 4.791 Limit: 4.660
*** Shift outlier: 27 E HA Secondary Shift: -1.698 Limit: -1.080
*** Shift outlier: 29 A C Secondary Shift: 4.021 Limit: 3.727
*** Shift outlier: 35 N C Secondary Shift: 4.104 Limit: 3.727
*** Shift outlier: 51 T HA Secondary Shift: 1.197 Limit: 1.047
*** Shift outlier: 52 F HA Secondary Shift: 1.164 Limit: 1.047
*** Shift outlier: 54 V CA Secondary Shift: -4.355 Limit: -3.445
*** Shift outlier: 56 E N Secondary Shift: 10.828 Limit: 10.047
*** C shift referecing offset: -1.289 ppm
Checking and preparing files …
MFR fragments searching … (may take a few hours…)
Done! MFR fragment tables farg9.t000.mfr.tab and frag3.t000.mfr.tab generated.

Converting to ROSETTA fragments …
9mer fragments …
Checking MFR Fragments Candidates …
200 fragments candidates for target fragment 1-9
200 fragments candidates for target fragment 2-10
200 fragments candidates for target fragment 3-11
200 fragments candidates for target fragment 4-12
200 fragments candidates for target fragment 5-13
200 fragments candidates for target fragment 6-14
200 fragments candidates for target fragment 7-15
200 fragments candidates for target fragment 8-16
200 fragments candidates for target fragment 9-17
200 fragments candidates for target fragment 10-18
200 fragments candidates for target fragment 11-19
200 fragments candidates for target fragment 12-20
200 fragments candidates for target fragment 13-21
200 fragments candidates for target fragment 14-22
200 fragments candidates for target fragment 15-23
200 fragments candidates for target fragment 16-24
200 fragments candidates for target fragment 17-25
200 fragments candidates for target fragment 18-26
200 fragments candidates for target fragment 19-27
200 fragments candidates for target fragment 20-28
200 fragments candidates for target fragment 21-29
200 fragments candidates for target fragment 22-30
200 fragments candidates for target fragment 23-31
200 fragments candidates for target fragment 24-32
200 fragments candidates for target fragment 25-33
200 fragments candidates for target fragment 26-34
200 fragments candidates for target fragment 27-35
200 fragments candidates for target fragment 28-36
200 fragments candidates for target fragment 29-37
200 fragments candidates for target fragment 30-38
200 fragments candidates for target fragment 31-39
200 fragments candidates for target fragment 32-40
200 fragments candidates for target fragment 33-41
200 fragments candidates for target fragment 34-42
200 fragments candidates for target fragment 35-43
200 fragments candidates for target fragment 36-44
200 fragments candidates for target fragment 37-45
200 fragments candidates for target fragment 38-46
200 fragments candidates for target fragment 39-47
200 fragments candidates for target fragment 40-48
200 fragments candidates for target fragment 41-49
200 fragments candidates for target fragment 42-50
200 fragments candidates for target fragment 43-51
200 fragments candidates for target fragment 44-52
200 fragments candidates for target fragment 45-53
200 fragments candidates for target fragment 46-54
200 fragments candidates for target fragment 47-55
200 fragments candidates for target fragment 48-56
Collecting structural information … Done (2908)!
Creating Rosetta fragments … Done!
3mer fragments …
Checking MFR Fragments Candidates …
200 fragments candidates for target fragment 1-3
200 fragments candidates for target fragment 2-4
200 fragments candidates for target fragment 3-5
200 fragments candidates for target fragment 4-6
200 fragments candidates for target fragment 5-7
200 fragments candidates for target fragment 6-8
200 fragments candidates for target fragment 7-9
200 fragments candidates for target fragment 8-10
200 fragments candidates for target fragment 9-11
200 fragments candidates for target fragment 10-12
200 fragments candidates for target fragment 11-13
200 fragments candidates for target fragment 12-14
200 fragments candidates for target fragment 13-15
200 fragments candidates for target fragment 14-16
200 fragments candidates for target fragment 15-17
200 fragments candidates for target fragment 16-18
200 fragments candidates for target fragment 17-19
200 fragments candidates for target fragment 18-20
200 fragments candidates for target fragment 19-21
200 fragments candidates for target fragment 20-22
200 fragments candidates for target fragment 21-23
200 fragments candidates for target fragment 22-24
200 fragments candidates for target fragment 23-25
200 fragments candidates for target fragment 24-26
200 fragments candidates for target fragment 25-27
200 fragments candidates for target fragment 26-28
200 fragments candidates for target fragment 27-29
200 fragments candidates for target fragment 28-30
200 fragments candidates for target fragment 29-31
200 fragments candidates for target fragment 30-32
200 fragments candidates for target fragment 31-33
200 fragments candidates for target fragment 32-34
200 fragments candidates for target fragment 33-35
200 fragments candidates for target fragment 34-36
200 fragments candidates for target fragment 35-37
200 fragments candidates for target fragment 36-38
200 fragments candidates for target fragment 37-39
200 fragments candidates for target fragment 38-40
200 fragments candidates for target fragment 39-41
200 fragments candidates for target fragment 40-42
200 fragments candidates for target fragment 41-43
200 fragments candidates for target fragment 42-44
200 fragments candidates for target fragment 43-45
200 fragments candidates for target fragment 44-46
200 fragments candidates for target fragment 45-47
200 fragments candidates for target fragment 46-48
200 fragments candidates for target fragment 47-49
200 fragments candidates for target fragment 48-50
200 fragments candidates for target fragment 49-51
200 fragments candidates for target fragment 50-52
200 fragments candidates for target fragment 51-53
200 fragments candidates for target fragment 52-54
200 fragments candidates for target fragment 53-55
200 fragments candidates for target fragment 54-56
Collecting structural information … Done (4027)!
Creating Rosetta fragments … Done!

Generating ROSETTA path file …
Generating ROSETTA running script …

Fragment Candidates Ready!
Go to rosetta, and type runRosetta3.com to run ROSETTA(3.X)!

===================

However, when I go to the just generated rosetta folder and run “runRosetta3.com”, I got errors:

usersxxx:rosetta>runRosetta3.com
ERROR: Option matching -in::file::frag3 not found in command line top-level context

—> I checked the Rosetta 3 command list and edit the “runRosetta3.com”, replace all double colons “::” by single colons “:” and save it. The edited “runRosetta3.com” is running now.

–> After testing, taking off one colon is necessary to run CS-rosetta well on my iMac.

12/23/2010

update: 1/27/2011

May 3, 2008

Cara 1.8.4.2 starts to support Mac OS X aqua

Filed under: mac,softwares and scripts — kpwu @ 7:51 am
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I didn’t notice the news (Cara has Mac OSX aqua version) until I helped a friend install Cara on his new macbook pro (leopard).

From Cara’s release news page, the last update date was 2007/4/26 (one year ago) which doesn’t show any information of supporting the native Mac OS X user interface. But I found there is an Alpha version using Mac OS X aqua interface listing in the Cara Download center.  It may not stable enough to be a daily-use NMR data analysis program, however, it’s a good news for Mac users that we don’t need to open X-window first.

2008/5/3

April 28, 2008

[software]-Magic Number Machine

Filed under: mac,softwares and scripts — kpwu @ 6:57 am
Tags:

I hate using the default calculator in dashboard of my Macbook pro. It’s not a clever program, as I feel.

In order to run some complicated math calculation, I searched and tested some calculator-like programs. This software (Magic Number Machine) has a very clear interface and nice design. I like it.

Office site: http://magicnumbermachine.googlepages.com/

Screenshot:

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