tag:blogger.com,1999:blog-9015174234871442237.post7477311627444934715..comments2024-03-17T00:33:08.666-07:00Comments on The art of blowing up protein: Everything you wanted to know about isopeptide bonds in Rosetta, but were too afraid to askMatteo Ferlahttp://www.blogger.com/profile/04090452288769979595noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-9015174234871442237.post-57948894737573671152021-12-06T02:41:46.634-08:002021-12-06T02:41:46.634-08:00The option string for the `init` function in PyRos...The option string for the `init` function in PyRosetta is the same as the command line in a Rosetta binary: you can repeat the command "-extra_res_fa foo.params -extra_res_fa bar.params" or add multiple entries to it "-extra_res_fa foo.params bar.params". I should mention that the arguments for `init` are options='-ex1 -ex2aro', extra_options='', set_logging_handler=None, notebook=None, silent=False. So it is best to call `pyrosetta.init(extra_options='-๐พ๐พ ๐พ๐พ -๐พ๐พ ๐พ๐พ')`.<br /><br />There is not a CYX params? Curious. "Traditionally" CYD is an cystine bonded cysteine, while CYX (and any other **X residues) is a crosslinked residue, however, Rosetta does not really care when the PDB input has a SSBOND or a LINK record. So if you have say an Alexa 488 maleimide crosslinked cysteine, you could use a regular CYS with a LINK record in your PDB โbut the thiol proton (HG) may be there IIRC. But to answer your question, copying the cys.params, changing the name to `CYX`, changing `IO_STRING CYX C`, adding `VARIANT SIDECHAIN_CONJUGATION`, removing the `ATOM HG` line, adding a `CONNECT SG ` line and changing all instances of ` HG ` to `CONN3` in the dihedral definitions block. Should do it.<br /><br />I had a gander at CYV. "CYS withVCB andVSG defined as virtual". I have no idea why the beta and gamma carbons are virtual... My guess it was for someone's experiment/proof-of-concept. So best ignored.<br /><br />Sorry for the tardy reply โmost comments are spam.Matteo Ferlahttps://www.blogger.com/profile/04090452288769979595noreply@blogger.comtag:blogger.com,1999:blog-9015174234871442237.post-51910484574613822522021-12-01T20:53:21.805-08:002021-12-01T20:53:21.805-08:00Hi.Do you know how to init pyrosetta with multiple...Hi.Do you know how to init pyrosetta with multiple params? For example, I have two residues protonated (CYX\HIP) and made params file for them. How can I add them to pyrosetta.init(-extra_res_fa)? Meanwhile, do you know how to make CYX params? I noted that there are CYZ and CYV in rosetta/xx/residue_tpyes, can you tell the difference? Thank you.Eileenbyhttps://www.blogger.com/profile/15426250603475381266noreply@blogger.com