Proteins, ProteinData, WolframAlpha

Question

Apologies in advance, this is the first I've messed with ProteinData and access through WolframAlpha, so clearly I may not know how Mathematica and Alpha decide on what is the 'right way' to ask for things of this ilk.

I'd like to grab ProteinData[], specifically a 3D model of the "RibbonStructure", of rhodopsin.

I can easily get a low-resolution, static image from Alpha, directly in Mathematica:

but I'd prefer the manipulatable 3D sort one gets from ProteinData[], since this is much better for classroom demos, interactive explanation, etc.

So, I try to look up rhodopsin via ProteinData in a wide variety of ways, by name, by PDB name, nada-

Let's try an alias ---

Success! But, there is no MoleculePlot

It knows a few things about "RHO", but not the things I need; and, more importantly, what Alpha is able to return.

So I'm at a loss here. I've tried other aliases ("OPN2", "visual purple") to no avail. I'm curious about ---

• Is there any way to figure out what WolframAlpha is doing with my request, since it can clearly interpret rhodopsin or rhodopsin protein?

• Is there a better way to use ProteinData than just randomly trying things? Is there a mapping somewhere of PDB <-> aliases, etc?

• Is there a way to as Alpha to return a higher resolution image than the sort-of-lame 320× I get? I know how to ask for just that pod, but it's unclear if there are any ways of asking for better / different pod content.

Answer 1

Here's a workaround that directly queries the PDB search API and returns the first num search results as a Dataset[]. The routine is more complicated than I'd like, due to the finicky nature of the API (it only takes queries in XML format), as well as the somewhat clunky way XML is represented in Mathematica:

pdbFindMoleculeName[name_String, num : (_Integer?Positive) : 10] := 
   Module[{query, res},
          query = XMLObject["Document"][{
                  XMLObject["Declaration"]["Version" -> "1.0", "Encoding" -> "UTF-8"]},
                  XMLElement["orgPdbQuery", {},
                  {XMLElement["queryType", {}, {"org.pdb.query.simple.StructTitleQuery"}],
                   XMLElement["struct.title.comparator", {}, {"contains"}],
                   XMLElement["struct.title.value", {}, {name}]}], {}];

          res = URLRead[HTTPRequest["http://www.rcsb.org/pdb/rest/search/",
                <|"ContentType" -> "application/x-www-form-urlencoded", 
                  "Body" -> ExportString[query, "XML"], "Method" -> "POST"|>]];

          If[! FailureQ[res], res = Import[res];
             If[res =!= "null", res = DeleteDuplicates[Flatten[res]];
                res = Dataset[AssociationThread[{"PDB ID", "Title", "Structure"},
                {#, Cases[Import["http://www.rcsb.org/pdb/rest/describePDB?structureId=" <>
                                 #, "XML"], ("title" -> t_) :> t, ∞][[1]], 

                 Import["https://files.rcsb.org/download/" <> # <> ".pdb", "PDB"]}] & /@
                Take[res, UpTo[num]]],
                res = Failure["NoResults",
                <|"MessageTemplate" :> "No results found for `name`", 
                  "MessageParameters" -> <|"name" -> name|>|>]]];
          res]

As a demo:

rhod = pdbFindMoleculeName["bovine rhodopsin"]

Of course, the Dataset[] format allows for convenient querying; e.g., if you want to see the structure of 1HZX:

First[rhod[Select[#"PDB ID" === "1HZX" &], "Structure"]]

Answer 2

Try this here

Import["http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1U19", "PDB"]

Answer 3

A quick and dirty is to download the PDB file from the main PDB database (eg Bovine rhodopsin), use the Download button/dropdown on the top right and select Text format then

rhodopsin= Import["DownloadedFileAndPath","Rendering"->"Structure"]

Naturally, you could get Mathematica to do the download too.

Options for alternate renderings can be found in the documentation for PDB format