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anybody know of some great free molecular graphics systems that can allow for PDB code input? I prefer that it doesn't use Java. I also prefer that it is online, although if there is a great system that has a simple download process, please share with me.

I am looking into trying to display a clear stick (or vines) version of one of the chains of a protein. I want a program that can help me easily do this.

I have tried using FirstGlance and Protein Workshop, but FirstGlance is kind of hard to navigate through and the Protein Workshop doesn't allow me to do stick models.

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    $\begingroup$ Have a look at Pymol and Chimera... $\endgroup$ – Gerhard Aug 13 '15 at 18:37
  • $\begingroup$ There are inofficial Windows builds of Pymol, those are free. Compiling Pymol yourself on Windows is very difficult, it's pretty doable on Linux. $\endgroup$ – Mad Scientist Aug 13 '15 at 20:10
  • $\begingroup$ There's also UnityMol, reads PDBs, Cytoscape networks, OpenDX potential maps, and Wavefront OBJ. $\endgroup$ – jzx Aug 13 '15 at 22:14
  • $\begingroup$ VMD is very powerful. $\endgroup$ – ddiez Aug 14 '15 at 3:26
  • $\begingroup$ which capabilities do you expect to have? $\endgroup$ – Ooker Aug 14 '15 at 5:59
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This is an answer simply because I can't fit it all in a comment, or several...

To install and run PyMOL, you'll need a few extras. They are all free and open-source:

  • Python 2.7.10: Make sure you choose to install pip during the setup process, and also choose to add Python to your PATH, if that option is given. Also, note whether you installed the 32-bit version (x86 MSI installer) or the 64-bit one (x86_64). Which you choose depends on your operating system - if you have a 32-bit OS, you only have one choice. If you have 64-bit Windows, you can do either one - there's no real difference to the casual user. I like 64-bit, but I'm a nerd :)

  • The numpy+mkl package: I'd get version 1.9.2, as 1.10.0b1 is a beta version. Make sure it's not one of the "unoptimized" builds! You want the cp27 (stands for CPython 2.7) package, either 32- or 64-bit, matching your choice above.

  • From the same page, the PMW package (choose the py2 version).

  • Finally, PyMOL itself (both pymol and pymol_launcher packages for cp27).

Once you have everything downloaded and Python installed, open the command prompt by hitting WinR, typing cmd into the box, and hitting Enter. Use the cd command to change to the directory where you downloaded the .whl files (paths with spaces in them should be completely enclosed in double quotes: cd "C:\Users\John Smith\Downloads"). Next, type pip -V to ensure pip works. If it doesn't, just use the whole path: C:\Python27\Scripts\pip -V. Once you get the version statement, you're good to go. For each filename, type pip install really_long_filename.whl to install it. Remember that you can start typing a long name, then hit Tab to complete it. Do this for all four wheels - numpy+mkl, pmw, pymol, and pymol_launcher - in that order.

Once you do that, you should be all set. I'm not on Windows at the moment, so I can't tell you whether you'll get an icon or not, but if you don't, then open Windows Explorer and browse to the C:\Python27\Scripts directory - there may be a PyMOL script there you can run.

If you have any questions, please ask on Stack Overflow, tagging the question with [python] and [pymol]. People are generally very quick with comments and/or answers, so please stick around on the question's page for 5 or 10 minutes to assist those who would help you.

Good luck!

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  • $\begingroup$ Is the MKL part important? I have numy but not MKL.. $\endgroup$ – TanMath Aug 14 '15 at 4:09
  • $\begingroup$ I'd recommend it, as the MKL can offer quite significant improvement in some numerical calculations over standard math libraries, and since PyMOL is completely based on very computationally-intensive work (displaying molecules and proteins in 3D), I'd strongly suggest getting it. To install over your current version of numpy, just run pip install -U numpy-1.9.2+mkl-blah-blah-blah.whl. The -U flag means "upgrade". $\endgroup$ – MattDMo Aug 14 '15 at 4:14
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Another good alternative is Swiss-PDB viewer. It is free, small, easy to install/use and is available for different OS (I had used it in Windows XP with 256MB RAM! Some features don't work well with low RAM but nonetheless it is not very resource hungry). It is good for the kind of tasks you are interested in. But it is not online (Actually I fail to understand why you need an "online" viewer).

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