CA = Carbon, Alpha (1st) CB = Carbon, Beta (2nd) CG, OG = Carbon/Oxygen, Gamma (3rd) CD = Carbon, Delta (4th) CE, NE, OE = Carbon/Nitrogen/Oxygen, Epsilon (5th) NZ = Nitrogen, Zeta (6th) NH = Nitrogen, Eta (7th) |
O3', O5' = 3' and 5' pentose oxygens C1' to C5' = 1' to 5' pentose carbons C2-C8, N1-N9, O2-O6 = elements in bases C5M = C5 Methyl (in Thymine) |
Ala A Alanine
Arg R Arginine Asn N Asparagine Asp D Aspartic acid (mnemonic: asparDic) Cys C Cysteine |
Gln Q Glutamine (mnemonic: Quetamine) Glu E Glutamic acid (mnemonic: gluEtamic) Gly G Glycine His H Histidine Ile I Isoleucine |
Leu L Leucine
Lys K Lysine (mnemonic: liKesine) Met M Methionine Phe F Phenylalanine (mnemonic: Fenylalanine) Pro P Proline |
Ser S Serine
Thr T Threonine Trp W Tryptophan (mnemonic: tWyptophan) Tyr Y Tyrosine Val V Valine |
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Appearance of a protein model that contains only alpha-carbon atoms (1A1D). |
Resolution, Å | Grade |
<1.6 | EXCELLENT |
1.6 - 1.79 | EXCELLENT/VERY GOOD |
1.8 - 1.99 | VERY GOOD |
2.0 - 2.29 | VERY GOOD/GOOD |
2.3 - 2.59 | GOOD |
2.6 - 2.89 | GOOD/FAIR |
2.9 - 3.19 | FAIR |
3.2 - 3.49 | FAIR/POOR |
3.5 or greater | POOR |
Resolution | Free R | ||
GoodQ | Median | BadQ |
Free R Value | Grade | |
<= (GoodQ - 0.02) | MUCH BETTER THAN AVERAGE at this resolution | |
------ GoodQ (best 25%) | > (GoodQ - 0.02) and <= ((GoodQ + Median)/2) | BETTER THAN AVERAGE at this resolution |
------ Median | > ((GoodQ + Median)/2) and <= ((Median + BadQ)/2) | AVERAGE at this resolution |
------ BadQ (worst 25%) | > ((Median + BadQ)/2) and <= (BadQ + 0.02) | WORSE THAN AVERAGE at this resolution |
> (BadQ + 0.02) | UNRELIABLE |
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Rationale: According to the rules for PDB files, all atoms that are not members of standard residues in protein or nucleic acid chains should be designated "hetero". Hetero atoms are typically further subdivided: there is "solvent" (water and some inorganic anions such as sulfate and phosphate), and everything else is "ligand". Rare PDB files don't follow the rules, and these confuse Jmol. And rarely, Jmol may interpret PDB files incorrectly. The result is atoms that are neither protein, nucleic acid, nor hetero. Within FirstGlance, these are deemed anomalous atoms.
Windows: Chrome 24 often started out with a blank black window. This appeared to be a bug.See also Firefox, Safari and Compatible Browsers.
Mac OS X: Safari is slightly preferable to Firefox and Chrome on Macs. The annoyance in Firefox is that right clicking in Jmol to open Jmol's menu unconditionally rotates the molecule a large amount. In the past there have ususally been other minor problems with Jmol in Firefox and Chrome.See also Safari, Chrome, Internet Explorer, and Compatible Browsers.
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