Question: Lightweight Structure Viewer, Callable From Linux Command Line
4
gravatar for Lyco
8.3 years ago by
Lyco2.3k
Germany
Lyco2.3k wrote:

Can someone recommend a simple structure viewer that can be easily called from the command line (like e.g. rasmol) for viewing pdb files stored in the current directory:

$ rasmol 1ubq.pdb

We work a lot from the command line and have a rather complicated directory hierarchy with some locally stored pdb files. I am aware of several good structure viewers running under X11, but they don't support the concept of a unix-style 'current directory' but open a 'load menu' instead that requires the user to nagivate through the directory hierarchy. Rasmol is one possibility, but I would prefer to have a viewer that also offers a 'sequence window' in addition to the structure display.

I should add that we are working behind a pretty restrictive firewall, so programs that require loading stuff from the net will not work.

viewer structure command-line • 2.1k views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 8.3 years ago by Lyco2.3k
1

Isn't PyMol lightweight enough for you?

ADD REPLYlink written 8.3 years ago by Jan Kosinski1.6k

can you see http://www.pdb.org/pdb/images/1ubq_bio_r_500.jpg behind your firewall ?

ADD REPLYlink written 8.3 years ago by Pierre Lindenbaum122k

Yes, HTTP via port 80 is permitted. The problem isn't really that the firewall is so restrictive. The main problem is that it requires authentification, which is ok in a browser but most other programs don't cope with that.

ADD REPLYlink written 8.3 years ago by Lyco2.3k

The last time I checked PyMol was free only for users at non-profit sites. Maybe this has changed? I will have a look.

ADD REPLYlink written 8.3 years ago by Lyco2.3k

Ok, that may be a problem. But I think that PyMol is free even for corporate organizations as long as you get it from svn and compile yourself, which is not difficult...

ADD REPLYlink written 8.3 years ago by Jan Kosinski1.6k

Ok, I have checked it and there seems to be a version that is free for everyone. It comes as a 41MB tarball (lightweigth enough) and requires me to install python and a lot of other packages (including the -dev pacakages, which I first forgot to do). In the end, the compilation crashes with an 'internal compiler error':

layer1/Scene.c:4565:11: internal compiler error: in set_jump_prob, at stmt.c:2319

Since I did not intend to learn python or C, I will have to wait for other suggestions :-(

ADD REPLYlink written 8.3 years ago by Lyco2.3k
7
gravatar for Leo
8.3 years ago by
Leo70
Heidelberg, Germany
Leo70 wrote:

I suggest you give VMD a try: http://www.ks.uiuc.edu/Research/vmd/

I believe it fits all your requirements (except perhaps the lightweight part):

  • You can run it from the command line:

    $ vmd 1ubq.pdb

  • It has a sequence viewer (Extensions -> Analysis -> Sequence Viewer)

  • Nothing needs to be downloaded over the internet, except if you want to use the more advanced sequence analysis plugin MultiSeq, which does download metadata using HTTP.

  • It's free of charge

ADD COMMENTlink written 8.3 years ago by Leo70

Thanks! I will check VMD.

ADD REPLYlink written 8.3 years ago by Lyco2.3k

I tried it and it works! Looks a bit idiosyncratic, but it should do the job. On the downside: when fooling around with some of the options (contact map display, I think) enlarging the window crashed my entire kde session. I haven't seen something like this in years.

ADD REPLYlink written 8.3 years ago by Lyco2.3k

Ouch, sorry to hear that. Maybe it's a bug in the video driver? I'd make sure it is up-to-date.

ADD REPLYlink written 8.3 years ago by Leo70
6
gravatar for Philippe
8.3 years ago by
Philippe1.9k
Barcelona, Spain.
Philippe1.9k wrote:

Hi,

I'm not expert in this field but it seems Jmol (using JVM to run) can do it. You first have to make the jmol.sh file executable (depends on your OS maybe, it was not the case on my computer) and launch the following command:

./jmol.sh 1ubq.pdb

You can of course change your $PATH to make it executable from any folder, including the one containing your pdb files.

Unfortunately it does not seem you can see the linear sequence of the protein. But, as I said, I am not expert with this software so it might still be possible. Additionally, in principle, nothing has to be loaded from the net.

ADD COMMENTlink written 8.3 years ago by Philippe1.9k

Thanks, I will give it a try.

ADD REPLYlink written 8.3 years ago by Lyco2.3k
1
gravatar for Khader Shameer
8.0 years ago by
Manhattan, NY
Khader Shameer18k wrote:

You can try MolScript / Raster3D

Both are command-line, no X-window / non-GUI, yet powerful tools for visualization. You can easily integrate your pipelines for automated visualization. But you don't get a sequence window with them.

Also, please see my answers on macromolecular visualization tools here and here for examples.

ADD COMMENTlink modified 7.3 years ago by Istvan Albert ♦♦ 81k • written 8.0 years ago by Khader Shameer18k
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