Background Although mmCIF is the current official format for deposition of protein and nucleic acid structures to the protein data bank (PDB) database, the legacy PDB format is still the primary supported format for many structural bioinformatics tools. Therefore, reliable software to convert mmCIF structure files to PDB files is needed. Unfortunately, existing conversion programs fail to correctly convert many mmCIF files, especially those with many atoms and/or long chain identifies. Results This study proposed BeEM, which converts any mmCIF format structure files to PDB format. BeEM conversion faithfully retains all atomic and chain information, including chain IDs with more than 2 characters, which are not supported by any existing mmCIF to PDB converters. The conversion speed of BeEM is at least ten times faster than existing converters such as MAXIT and Phenix. Part of the reason for the speed improvement is the avoidance of conversion between numerical values and text strings. Conclusion BeEM is a fast and accurate tool for mmCIF-to-PDB format conversion, which is a common procedure in structural biology. The source code is available under the BSD licence at https://github.com/kad-ecoli/BeEM/ .
Abstract Although mmCIF is the current official format for deposition of protein and nucleic acid structures to the Protein Data Bank (PDB) database, the legacy PDB format is still the primary supported format for many structural bioinformatics tools. Therefore, reliable software to convert mmCIF structure files to PDB files is needed. Unfortunately, existing conversion programs fail to correctly convert many mmCIF files, especially those with many atoms and/or long chain identifies. This study proposed BeEM, which converts any mmCIF format structure files to PDB format. BeEM conversion faithfully retains all atomic and chain information, including chain IDs with more than 2 characters, which are not supported by any existing mmCIF to PDB converters. The conversion speed of BeEM is at least ten times faster than existing converters such as MAXIT and Phenix. BeEM is available under the BSD licence at https://github.com/kad-ecoli/BeEM/ .
# How many different chains exist within a specific pdb file?
Tags: proteins, pdb
- Score: 2
- Views: 754
- Answers: 1
- Answered: yes
- Asked by: Yasmin (23 rep)
- Asked: 2018-09-29
- Site: biology
## Question
More specifically, if we want to understand the different chains within a protein, is it enough to look at the fourth column of all the lines that start with "ATOM" in a pdb file, and see how many different chain identifiers exist there?
## Answers
### Answer by marcin (score: 0 [ACCEPTED])
In the PDB format the lines with atoms can start either with ATOM or HETATM.
Chain ID is in column 22, i.e. it is 22nd character of a line that starts with ATOM or HETATM. (Programs that support 2-character chain IDs use columns 21-22 − it's a popular extension of the PDB format).
Yes, the number of different chain IDs is the same as the number of "chains" in the PDB file.
But note that the "chain" from the PDB format is not necessarily a real chain (polymer). It may be a bunch of water molecules or something else.
# What is "chain identifier" in PDB?
- Tags: pdb
- Score: 6
- Views: 7,940
- Answers: 1
- Asked by: Reza (275 rep)
- Asked on: Sep 3, 2015
- Last active: Sep 10, 2015
- License: CC BY-SA 3.0
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## Question
The PDB file format is explained [here](http://deposit.rcsb.org/adit/docs/pdb_atom_format.html). My question is what "chain identifier" is exactly? What is the difference between two residues which have the same sequence number but different chain identifiers?
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## Accepted Answer — Score: 7
- By: MattDMo (15,366 rep)
- Answered on: Sep 4, 2015
The "chain identifier" does exactly what it says: it identifies the polypeptide or other molecular chain. For some structures, there is only one, so you'll only see an identifier `A`. However, many structures show two or more proteins bound together, or an enzyme complexed to a substrate, or a small molecule inhibitor in a binding pocket - there are many different possibilities. Each individual chain of atoms has its own identifier.
For example, [1VKX](http://www.rcsb.org/pdb/explore/explore.do?structureId=1VKX) shows my favorite transcription factor NF-κB bound to the κB DNA enhancer sequence. There are four chains in the stru
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