Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. It only takes a minute to sign up. Connect and share knowledge within a single location that is structured and easy to search. I have several pdb files and each of them corresponds to a domain on a protein.
I want to merge these files into one single pdb for the whole protein, and the approach I'm looking for should allow me to order these domains according to the order by which they're located on the protein for example, merging domain A, B, and C by the order CBA.
It would be preferable if I can do the merging with VMD but any suggestion would be appreciated. However, they will need to be the same chain and segment segi. Also you will need to fix the numbering to match what you expect them to be. To fix this you need to do:. PyMOL can be installed as a Python 3 module, which works in the same way but with pymol. But for starting out the App is fine. This assumed that the coordinates are where we want them to be. Which is highly unlikely and that there are zero overlaps.
If you want to add linkers, you can use submit your sequence to Phyre or I-Tasser with your missing density model as a reference, or you can add them with rosetta remodel tricky or make them up in Coot or PyMOL bad idea, but if you are in a hurry Sign up to join this community.
I think that is an easier solution than using PyMol, but I am sure you can do it in there as well probably somehow via the Python shell scripting. Is there a specific reason you want to use PyMol for this purpose? Here once you log in you will be able to sign up for the periodic email updates about this question.
How do you list H-bonds in pymol? How do you use PyMol to visualize structure bundles and related MR data? How to open multiple pdb files with PyMol - all at once? Whoops, see all those extra long bonds? So in a text editor it is a simple matter to remove them all.
The resulting edited PDB file can then be read back into Pymol without all those nasty extra lines, but…. This export-import routine introduces some weird forgetfulness about what secondary structural elements the protein contains.
So Pymol does nothing when you try and show a cartoon representation of the proteins. The normal thing to do in these circumstances is to run the util. I did this and got the famous Apple spinning beachball of death. But it was a long wait 20 minutes. This is a pretty good place to point out that this was all done in Pymol 1. But the process eventually ended up a failure.
Despite showing all the right messages in the log box, no secondary structural features could be obtained. So the process is not yet complete. I shall keep you posted. Stoermer, Keith J. Chappell, Susann Liebscher, Christina M. Jensen, Chun H. Gan, Praveer K. Young, and David P. Fairlie, J. Full text via ACS publications.
Young, David P. Fairlie, Jennifer L Martin J. Full text via ScienceDirect. Stoermer, David P. Fairlie, Bostjan Kobe, Paul R. Young Antiviral Research, , 84 3 , Science, , , Pubmed Link. The time is well past for the PDB format. Say hello to pdbx sometimes known as mmCIF. It is inherent in the file format. You are commenting using your WordPress.
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