Pull request #633: Replaced MMTF data with Binary CIF data. Both "mmtfid" and "bcifid" inputs get the Binary CIF data.

Merge in STRUC/icn3d from release3310 to master

* commit '86f65bedcbf78e4e8439a38854f675bee646100c':
  Replaced MMTF data with Binary CIF data. Both "mmtfid" and "bcifid" inputs get the Binary CIF data.
  Replaced MMTF data with Binary CIF data. Both "mmtfid" and "bcifid" inputs get the Binary CIF data.
  Replaced MMTF data with Binary CIF data. Both "mmtfid" and "bcifid" inputs get the Binary CIF data.

Author: jiywang3

CHANGELOG.md

@@ -1,4 +1,6 @@
 ## Change Log
+[icn3d-3.31.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.31.0.zip) was release on March 21, 2024. Replaced MMTF data with Binary CIF data. Both "mmtfid" and "bcifid" inputs get the Binary CIF data. 
+
 [icn3d-3.30.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.30.1.zip) was release on March 11, 2024. Fixed 3D domain summary view.
 
 [icn3d-3.30.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.30.0.zip) was release on February 27, 2024. Calculate 3D domains on-the-fly and show 3D domains even when only one domain is available.

README.md

@@ -83,7 +83,7 @@ iCn3D accepts the following IDs:
 * <b>mmdbafid</b>: A list of PDB or AlphaFold UniProt IDs for realignment, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbafid=1HHO,4N7N,P69905,P01942](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbafid=1HHO,4N7N,P69905,P01942). You can then input multiple PDB files with the menu "File > Open File > PDB Files (appendable)". Next you can click the menu "File > Realign Selection > by Structure Alignment" to realign all loaded structures.
 * <b>protein</b>: Protein/Gene name to search AlphaFold structures, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?protein=TP53&showanno=1&showsets=1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?protein=TP53&showanno=1&showsets=1)
 * <b>mmdbid</b>: NCBI MMDB ID, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbid=1tup&showanno=1&show2d=1&showsets=1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbid=1tup&showanno=1&show2d=1&showsets=1)
-* <b>mmtfid</b>: MMTF ID, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmtfid=1tup&show2d=1&showsets=1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmtfid=1tup&showanno=1&showsets=1)
+* <b>bcifid or mmtfid</b>: Binary CIF ID or MMTF ID, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=1tup&show2d=1&showsets=1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=1tup&showanno=1&showsets=1)
 * <b>pdbid</b>: PDB ID, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?pdbid=1tup&showanno=1&showsets=1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?pdbid=1tup&showanno=1&showsets=1)
 * <b>afid</b>: AlphaFold Structure with UniProt ID, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?afid=A0A061AD48&showanno=1&showsets=1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?afid=A0A061AD48&showanno=1&showsets=1)
 * <b>refseqid</b>: AlphaFold Structure with NCBI Protein Accession, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?refseqid=NP_001743.1&show2d=1&showsets=1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?refseqid=NP_001743.1&show2d=1&showsets=1)
@@ -94,7 +94,7 @@ iCn3D accepts the following IDs:
 * <b>align multiple chains</b>: any multiple chains for structure alignment, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?chainalign=1HHO_A,4N7N_A&showalignseq=1&show2d=1&showsets=1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?chainalign=1HHO_A,4N7N_A&showalignseq=1&show2d=1&showsets=1)
 * <b>blast_rep_id and query_id</b>: NCBI protein accessions of a protein sequence and a chain of a 3D structure for sequence-structure alignment, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?from=icn3d&blast_rep_id=1TSR_A&query_id=NP_001108451.1&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain 1TSR_A; show selection](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?from=icn3d&blast_rep_id=1TSR_A&query_id=NP_001108451.1&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain 1TSR_A; show selection)
 
-iCn3D also accepts the following file types: PDB, mmCIF, Mol2, SDF, XYZ, and iCn3D PNG. The files can be passed through a url, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=pdb&url=https://storage.googleapis.com/membranome-assets/pdb_files/proteins/FCG2A_HUMAN.pdb](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=pdb&url=https://storage.googleapis.com/membranome-assets/pdb_files/proteins/FCG2A_HUMAN.pdb), [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=mmcif&url=https://files.rcsb.org/view/1GPK.cif](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=mmcif&url=https://files.rcsb.org/view/1GPK.cif), or [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=icn3dpng&url=https://api.figshare.com/v2/file/download/39125801](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=icn3dpng&url=https://api.figshare.com/v2/file/download/39125801). See the [help page](https://www.ncbi.nlm.nih.gov/Structure/icn3d/docs/icn3d_help.html) or the [Doc page](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html) for more details.
+iCn3D also accepts the following file types: PDB, mmCIF, Mol2, SDF, XYZ, and iCn3D PNG. The files can be passed through a url, e.g., [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=pdb&url=https://storage.googleapis.com/membranome-assets/pdb_files/proteins/FCG2A_HUMAN.pdb](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=pdb&url=https://storage.googleapis.com/membranome-assets/pdb_files/proteins/FCG2A_HUMAN.pdb), [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=mmcif&url=https://files.rcsb.org/download/1GPK.cif](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=mmcif&url=https://files.rcsb.org/download/1GPK.cif), or [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=icn3dpng&url=https://api.figshare.com/v2/file/download/39125801](https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=icn3dpng&url=https://api.figshare.com/v2/file/download/39125801). See the [help page](https://www.ncbi.nlm.nih.gov/Structure/icn3d/docs/icn3d_help.html) or the [Doc page](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html) for more details.
 
 ## Third-party libraries used in Frontend