Renumbering PDB files: Difference between revisions
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==PDBrenum== | ==PDBrenum== | ||
[http://dunbrack3.fccc.edu/PDBrenum/ PDBrenum] is a server that renumbers atomic coordinate files to match the numberings in the corresponding [http://uniprot.org UniProt] entries. PDBrenum will process both [[PDB file format]] and [[atomic coordinate file|mmCIF file format]] atomic coordinate files. | [http://dunbrack3.fccc.edu/PDBrenum/ PDBrenum] is a server that renumbers atomic coordinate files to match the numberings in the corresponding [http://uniprot.org UniProt] entries. PDBrenum will process both [[PDB file format]] and [[atomic coordinate file|mmCIF file format]] atomic coordinate files.<br/> | ||
There is a scientific article describing PDBrenum<ref>PMID: 34228733</ref> that shows it can be run as a Python script as well. | |||
In the example of [[6ef8]] vs. [[6nef]], after processing by PDBrenum, the cytochromes in both files have sequence numbers 26-432, which is very helpful. Unfortunately, the authors listed the hemes (HEC) in different orders in the text of the PDB files, so their numbers still don't match. | In the example of [[6ef8]] vs. [[6nef]], after processing by PDBrenum, the cytochromes in both files have sequence numbers 26-432, which is very helpful. Unfortunately, the authors listed the hemes (HEC) in different orders in the text of the PDB files, so their numbers still don't match. | ||
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#At the bottom, click the green '''Run''' button. | #At the bottom, click the green '''Run''' button. | ||
The output is a PDB file containing only chain A, renumbered 26-432. The HEC groups are also renumbered. To avoid renumbering those, you would have to delete them and then cut/paste from the original PDB file using a [[Help:Plain text editors|plain text editor]]. | The output is a PDB file containing only chain A, renumbered 26-432. The HEC groups are also renumbered. To avoid renumbering those, you would have to delete them and then cut/paste from the original PDB file using a [[Help:Plain text editors|plain text editor]]. | ||
==References== | |||
<references /> | |||
