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Thanks so much when I used the browse button instead of just typing the file name it worked fine. We are having a high school open house coming up so I am trying to print a model of GFP (PDB: 1GFL) Sadly I am terrible with programming things so I have difficulty troubleshooting in with anything DOS. I really like how on the SH2 domain you have secondary structures what drawing method did you used for that? I was able to use polyhedral to get really great looking beta sheets in the beta can fold but I am afraid the connecting loops might be too thin and there isn't a radius option with that one. Do you have a suggestion for the method I should use? I would like the students to be able to see how GFP structure is a beta can which is a bit difficult to tell with the tube method.
I really appreciate your help. Everyone in the lab is fascinated with the printer. We are still having some problems with the PLC it was working great for a while after being in the dessicator at the end of each day. However now it seems to be acting up again not melting evenly or something. I am hoping our new filament will arrive soon and I can try a fresh spool.
It sounds like everything is working. What PDB are your trying to render? BTW I posted a version of CFP that is a bit easier to remove the scaffolding from.The file is being saved to where ever you have VML pointed to to save. Solutions: 1)search for the name you save the file as on your computer (in this case "gfp.stl" as shown in the Filename: box) and find out where the file is being saved (it is being made I believe) 2) in VML on the same line as filename: there is a button for browse. Click on this and select where you want the file to be saved. Let me know how this works out!
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There are over 40 different protein domains. The three dimensional structure of proteins and their domains is determined by x-ray crystallography or nuclear magnetic resonance (NMR). The 3D coordinates of each atom in a domain is determined and provided in a protein database (PDB) format. The PDB files for every proteins structure ever determined are freely available at PDB.org. Below is a brief description of ten different domains, followed by an explanation of how to take a PDB file and convert it to an STL file. A shout-out to PMOEWS whose work (thing:12283) inspired me and offered direction.
SH2 domain #1BFJ
Src-homology 2 (SH2) domains are modules of ~100 amino acids that bind to specific phospho tyrosine (pY) containing peptide motifs. Conventional SH2 domains have a conserved pocket that recognizes pY, and a more variable pocket that binds 3-6 residues C-terminal to the pY and confers specificity.
SH3 domain #1NEB
Src-homology 3 (SH3) domains bind to Pro-rich peptides that form a left-handed poly-Pro type II helix, with the minimal consensus Pro-X-X-Pro. Each Pro is usually preceeded by an aliphatic residue. Each in the aliphatic-Pro pair binds to a hydrophobic pocket on the SH3 domain.
CARD domain #1CY5
Caspase Recruitment Domains (CARDs) are modules of 90â€“100 amino acids involved in cell death (apoptosis) signaling pathways. CARDs mediate the association of adaptor proteins and procaspases (death proteins) through heterodimerization of their respective CARDs, recruiting procaspases to upstream signaling complexes and allowing autoactivation.
Death Domain #1DDF
Death domains (DD) are 80â€“100 residues long motifs involved in cell death (apoptotic) signal transduction. Death domains serve as recruiting modules through their ability to heterodimerize with the death domains of distinct proteins, including adaptor proteins such as FADD.
EF hand domain #2PMY
The EF-hand motif contains approximately 40 amino acids (residues) and is involved in binding intracellular calcium. Binding of calcium to regulatory EF-hand domainâ€”containing proteins induces a conformational change, which is transmitted to their target proteins, often catalyzing enzymatic reactions.
Beta barrel (cyan fluorescent protein) #4AR7
This fluorescent protein is a variation of green fluorescent protein from a jellyfish and is the only domain that is a complete protein. The protein is routinely used to visualize a variety of biological processes. The beta barrel domain is a beta sheet wrapped around the fluorescent active site to provide structure.
Ring domain #1CHC
The RING finger is a specialized type of Zn finger consisting of 40â€“60 residues that binds two atoms of zinc, and is involved in mediating proteinâ€”protein interactions. Many zinc fingers bind nucleic acids. The presence of a RING finger domain is a characteristic of RING-class E3 ubiquitin protein ligases capable of transferring ubiquitin from an E2 enzyme to a substrate protein.
WW domain #1EOM
WW domains are small 38 to 40 amino acid residue modules that have been implicated in binding to Pro-rich sequences.
Helix turn helix domain #3V1A
The helix-turn helix is a DNA-binding domain. The two alpha helices are the reading or recognition helices, which bind in a groove in the DNA and recognize specific gene regulatory sequences in the DNA. This pairs well with thing:17343 by emmett!
Ig domain #2CKN
This particular domain is named for the first protein in which it was found, the immunoglobulin. An immunoglobulin is a antibody. Antibodies are generated by our immune system to recognize the specific size, shape and charge of pathogens. This domain is also found on the extracellular portion of many receptors including the interleukin-1 family of receptors.
Convert pdb to stl file
Select structure from pdb.org
open VMD 1.9.1 (http://ks.uiuc.edu/Research/vmd/)
Load pdb file â†’file â€œnew moleculeâ€
â€œgraphicsâ€ â†’ representations â†’ drawing method â€œtubeâ€
Display â†’axes â†’ off
Fileâ†’ render â†’ â€œenter file nameâ€ â†’ STL â†’ render
Open in replicator G
Scale to appropriate size (many times very small and unseeable!)
Upload to cloud.nettfabb.com to fix stl
Slice and print!
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