Hello, I have a bit of a complicated query here and I'd much appreciate some help if possible.
I'm currently trying to make a 3D model of an antibody by using homology modeling. The issues I have, though, can be summarized in:
- I can't use free to use academic software since I'm working for a company.
- My company hasn't approved to buy Rosetta software license to use.
These two issues aside, I would be ok if I ended with at least an approximated representation of my antibody by making all the steps by myself (which as you can imagine is highly time-consuming).
I do have the .pdb file for the variable regions for both light and heavy chains and the full aminoacid sequence of my antibody. I've already performed some alignments and downloaded the corresponding pdb files for the homologous antibody that I'm going to use as a template for each light and heavy chain separatedly, and here is where I've encountered the most problem. I've been able to modify the light chain files, however, when it comes to modify the heavy chain, I find that the final structure I get has a whole disconnected section from the main body of the antibody. I have made a big substitution there, 118 residues, therfore I've had to renumber the serial number from the ATOM lines for it to fit correctly. I think that maybe the coordinates provided are just not fitting inside the whole antibody template frame and thus it's giving me this inconsistency. However, I can't figure out if I should be merging the pdf files in a different way or if it is just not possible to do this kind of merging? What surprises me is that the light chains have no problems regarding this aspect...
What I'm doing is using notepad++ to modify the files separatedly. I have seen that some use PyMOL to do such changes however I have also read that making changes using an editor would theoretically be just as good, only maybe a bit more messy. Is this right or am I ignoring a tool that could be of help to solve my problem?
Thanks in advance and sorry for the long post.
This isn't much of an answer, but I'd just mention that not all academic software will be chargeable for companies, so don't give up entirely on academic software. Here are a few tools that might help (in no particular order, and I have no idea what their license setups are - some will require a different license for companies, but they may still be free):
As for editing the PDB directly. As with most bioinformatics formats, they're just plain text, so there is no harm in using an editor per se if you know what you're doing. Just be careful not to munge the file formatting which would stop it being parsed in by other tools though.