User:Wayne Decatur/I-Ppo Morph Methods: Difference between revisions

So I searched for something else thinking although I could break it up and do it with a simple Python program it would be nice to find a tool or service to do it to which I could direct students and colleagues who have the same issues arise instead of having them install Python if they aren't already using it.)

I found [http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/ PDB Goodies] to take care of the chain renumbering. To get started, just a bit down the page I clicked the not overly obvious spot that said 'click here to see available options in PDB Goodies' to start and on the next page uploaded my pdb file. (Note on this page a link to <help> in the bottom right corner that does summarize what PDB Goodies does). And I chose 'Change Identifiers' and changed A and B to C and D easily using the form generated from my uploaded file and getting the results. (Note PDB goodies also renumbers residues numbers, generating a nice form using the file; I had problems when name of my uploaded file was very long (shortening name fixed it). )('''When helping people with animations previously I had used 'alter' command right in Pymol (see http://pymol.sourceforge.net/newman/ref/S1000comref.html) and ran 'sort' command after each altering in order to change chain designations in the pdb files, for example see [[User:Wayne Decatur/Sandboxmangai]]''') For renumbering the atom numbers I found [http://www.mayachemtools.org/docs/scripts/html/ModifyPDBFiles.html this page] of documentation for [http://www.mayachemtools.org/ Maya Chem Tools] which does a lot more manipulating of PDB files than just what I found it for but it is for installing with Perl. So having found a number of possibly useful items, I decided it was easier to write my own Python script because I realized that I also need to discard lines that involved atoms designated 'H5*' that I assume came from Model It and this is a fairly unique situation that shouldn't arise often for others.  

Next I combined the aligned edited 1evx file with the aligned edited unbound DNA file to match 1a73. At first I thought the [http://www2.molmovdb.org/wiki/info/index.php/Morph_Server Yale Morph Server] wouldn't work because I had DNA in the structure but in the FAQ I found a link to the [http://molmovdb.org/cgi-bin/multichain.cgi Morph Server for multiple subunits and nucleic acids] that sounded perfectly suited; however, it didn't seem to ever send anything back. So I went looking for more explanation and couldn't figure out what was wrong. So I looked at what the FAQ called 'the Beta server'. That server said on its page [http://www.molmovdb.org/cgi-bin/beta.cgi here] that is was the 'Server for morphing complexes' and they wanted to implement it working for nucleic acids "in a few weeks". (I also found that at the time, the link to the 'multi chain server' [http://www2.molmovdb.org/wiki/info/index.php/Morph_Server here] went to that server too.) On a lark, I tried it with the proteins (using the same file I submitted to the other server) and they came right back nicely morphed. Then I used it to submit the same files and they came back nicely morphed. IT WORKED.