With the program RasMol, you can select, as Mad Scientist explained it for PyMol, everything in a specific distance around an atom. RasMol can be run from command line, using a script (with the -script option under UNIX).
The residue numbering convention in the PDB is more-or-less entirely up to the depositor of the structure. While generally speaking sequential numbers are next to each other, there is no guarantee of that fact.
For example, the PDB allows for what are called "insertion codes", which are extra residues which interrupt the regular sequence progression. For ...
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 ...
You are making a few assumptions that are likely not valid for all PDB files. For example:
Residue indices are not necessarily sequential, nor do they have to start at 1
Not all possible residues have 1-letter code equivalents, there are thousands of possible exotic residues, not only the standard amino acids
PDB files are not only used for proteins, but ...
You may consider taking a look at the SCOP structural classification of proteins to check all beta proteins and all alpha proteins. As per specific examples and though not belonging to the SCOP classes mentioned above, Porin for a beta protein (PDB:1A0S), and Rhodopsin for an alpha protein (PDB:1F88) are two nice structures to look at.
Solving the 3D structure of a protein is hard and a lot of work, doing that for every common SNP of a protein would be excessive in most cases. So you generally won't find such structures unless the structure of the specific mutated version is particularly interesting.
In many cases it is also not structurally interesting what happens, there is no point in ...
ProDy works quite well, especially from within an existing Python script.
The following code takes an existing PDB file, performs some selection query on it, then saves it to another file.
def pdbsubset(inpdb, outpdb, selection):
with open(inpdb) as protf:
prot = prody.parsePDBStream(protf)
atoms = prot.select(selection)
TLDR; Answer: You could consider this particular residue to belong to both structural elements, but it's a tricky call and depends on the method of secondary structure assignment.
Ambiguous secondary structure allocation comes up fairly often. Whilst obviously, not many people will be able to use this protein specifically, the below approach could be useful ...
This is almost more a philosophical question about how you would like to define helices and sheets, which I would argue is not so well defined. shigeta mentions that they have well defined ramachandran coordinates, but that's for the central residues. Terminal residues are far more flexible. The more traditional definition is along the lines of the DSSP ...
There doesn't seem to be a 3D structure of Osteopontin available, and after looking a bit at the literature about this protein I'm not really surprised.
Osteopontin is hypothesized to assume an elongated and flexible structure (Sodek et al., 2000). Flexible proteins are very hard to impossible to crystallize, typically the flexible parts are either removed ...
Since you have the structures the best option, in my opinion, is Pymol.
Open Pymol. Load up your protein of choice. Download color_h.py which is a script from the University of Osaka that colours the residues according to Eisenberg's scale of hydrophobicity. Load this into Pymol by File->Run->PATH/TO/color_h.py. Then in Pymol run the ...
The pdb file that you mention is entitled:
V-Amylose at atomic resolution: X-ray structure of a cycloamylose with 26 glucose residues (cyclomaltohexaicosaose).
So, it isn't a protein at all, it is a circular oligosaccharide consisting of 26 glucose (GLC) residues. I imagine that the usual fields in the pdb file have been fudged to accommodate this.
The PDB file format was specified in the dawn of computing to fit on punch cards. So it has some shortcomings that have led to generations of scientists cursing the fixed-width column format. By now, it has been superseded by an XML-like format: PDBML. Of course XML is less space-efficient than a column layout, so you can see that disk space was not the main ...
These two links go through the specifications required for the PDB format:
Link1 primarily goes through the specs. required if you say have a NMR file you would therefore require the MODEL statement. It also goes through other statements such as when to use TER and how each ATOM line should look ...
Isoleucine only has one delta carbon, which we can just call CD. But it seems like some PDB files still name it CD1, and hence programs map CD1 to CD in this case. (E.g. see this tutorial where this practice is shown.)
I'm resurecting an old question, but I've heard this question from a few young bioinformaticians and had a couple more points to consider about compressing PDB files.
The first is that many PDB files (including all PDBs hosted on the PDB site) have some 300-400 lines of meta data at the top of the file. This accounts for about 10-20% of the total file size....
The article cited in the question indicates that the authors searched the PDB with the term “unknown function”. There is nothing special about this — you just type in the standard search field and hit ‘Go’. I conducted a search of this type myself:
Which returned 4384 structures ...
Chain IDs are assigned by authors who submit the structure to the wwPDB.
According to the PDB spec:
Non-blank alphanumerical character is used for chain identifier.
Usually, the chains are assigned uppercase letters.
But since digits and lowercase letters are also allowed, some people will use it.
And a good reason to allow more characters is to ...
I know the question is old, but for the record: the RCSB PDB is currently working on a project to compress the PDB structural data with a new file format, called MMTF (MacroMolecular Transmission Format).
The format uses MessagePack for serialization and does custom compression, achieving ~ 5x advantage over mmCIF gzipped files. Currently the whole PDB ...
PDB residues are described by the residue number and an insertion code. Residue numbers can be any number, including negative values. In 3CKR the first residue has nr. -6, followed by -5, etc. This might indicate that there are additional residues at the beginning of the sequence, relative to other PDB entries. In 2P83, the first residue has the number 61P. ...
There are no MTRIX cards for that molecule. This seems like the easiest path:
Download Files -> Biological Assembly 1
And read that file into Coot (should you wish)
You can find examples by using the "drilldown" function at the RCSB PDB homepage:
Click on the number 103921 at the top of the page at http://www.rcsb.org then find the "SCOP Classification" section and then e.g. select "All alpha proteins".
This may or may not be possible, depending on what proteins you are considering. Generating a PDB file means predicting the structure of the protein. There are no methods for predicting protein folding accurately from plain sequence data, so you will need some experimental data on the structure of your proteins.
If your proteins have not been structure ...
If there is a simple way provided to do this it is very well hidden. The tedious and stupid way to do 1 (get a list of folds) would seem to involve rolling your own:
Go to http://scop.berkeley.edu/ver=2.06 .
Click on each of the 12 classes in turn. e.g. (a) all alpha proteins will take you to http://scop.berkeley.edu/sunid=46456 .
Save the source of each ...
Your approach is correct but it is worth considering which database will work best for you. Questions to consider are;
Does the database provide a large search space for the organism(s) you're interested in?
Do its IDs work well for searching other databases?
How does the host database handle identifiers over time?
For protein sequences I would use;
If I remember correctly pymol can edit pdb structures (as well as visualize them).
I've used a student version though (which is a free full version) and I'm not quite sure if its possible to use pymol without buying a license nowadays (though the source code is still open source, so can in principle always install it from that)