DSSP through PyMol
I have been using DSSP from within PyMol through a nice plugin provided by Hongbo Zhu.
The plugin works nicely, of course, you have to previously install DSSP and Stride.
I got those from Fink in Mac OS X Snow Leopard but I think they are absent in Lion. In Lion, you can get whatcheck (which includes DSSP) through MacPorts.There used to be a dsssmcbi available that was easy to compile in Mac OS X but I think is gone from the web (update: I have mirrored that version here).
To compile dssp extract the compressed files and issue:
./DsspCompileCC
And that should be it.
And Stride source code is over here. I have compiled stride successfully with those files. All you have to do is uncompress it, cd into the the directory and issue a make command. If you already have Xcode installed you should have no problem getting an stride binary.
Remember that to have them working you should added them to your path (I prefer this) or copy them to your /usr/local/bin/
This blog entry also server the purpose to make clear that DSSP and Stride will fail to do anything if your PDB has no chain ID. Since I use a lot of homology models I have run into this problem twice and I want to point to the cause to avoid it later.
PS. comments are welcome.
The plugin works nicely, of course, you have to previously install DSSP and Stride.
I got those from Fink in Mac OS X Snow Leopard but I think they are absent in Lion. In Lion, you can get whatcheck (which includes DSSP) through MacPorts.
To compile dssp extract the compressed files and issue:
./DsspCompileCC
And that should be it.
And Stride source code is over here. I have compiled stride successfully with those files. All you have to do is uncompress it, cd into the the directory and issue a make command. If you already have Xcode installed you should have no problem getting an stride binary.
Remember that to have them working you should added them to your path (I prefer this) or copy them to your /usr/local/bin/
This blog entry also server the purpose to make clear that DSSP and Stride will fail to do anything if your PDB has no chain ID. Since I use a lot of homology models I have run into this problem twice and I want to point to the cause to avoid it later.
PS. comments are welcome.
Comments
The dssp was working wonderfully before I managed to delete the link of dssp from /opt/local/bin. Now dssp works from /opt/local/share/whatcheck/dssp but I can't globally access it as I could earlier, by just typing "dssp *.pdb". Should adding the path to .profile help?
Thanks in advance
Adding dssp to your .profile or .bashrc will help.
Try .profile first. If that doesn't work, use the .bashrc instead.
Best regards