How to Use FirstGlance |
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 |
***** SAMPLE FOR 2ACE ***** S C S C SEQCRD 0 D ASP --- 1 - - - 367 Key to 3-Letter Codes SEQCRD 0 D ASP --- 2 - - - 367 SEQCRD 0 H HIS --- 3 - - - 367 <-- THIS LISTING IS NOT FOR YOUR MOLECULE! SEQCRD 0 S SER SER 4 4 C T 5 EXAMPLE AT LEFT IS FOR 2ACE. SEQCRD 0 E GLU GLU 5 5 C T 5 FOR YOUR MOLECULE, [lines 6-482 omitted] SEQCRD 0 N ASN ASN 483 483 C T 5 SEQCRD 0 E GLU GLU 484 484 C T 5 SEQCRD 0 P PRO --- 485 - - - 367 SEQCRD 0 H HIS --- 486 - - - 367 SEQCRD 0 S SER --- 487 - - - 367 SEQCRD 0 Q GLN --- 488 - - - 367 SEQCRD 0 E GLU --- 489 - - - 367 SEQCRD 0 S SER SER 490 490 C T 5 SEQCRD 0 K LYS LYS 491 491 C T 5 [lines 492-533 omitted] SEQCRD 0 A ALA ALA 534 534 H H - SEQCRD 0 T THR THR 535 535 H C 5 SEQCRD 0 A ALA --- 536 - - - 367 SEQCRD 0 C CYS --- 537 - - - 367The conclusion from the above listing is that residues 1-3, 485-489, and 536-537 lack coordinates. In a long S2C listing such as the one above, you can use your browser's Find in page with the search word "---" to jump to any gaps.
4, 484, 490, 535into the Find.. slot and press Enter. You will be able to see the gap in the chain, marked by halos. By clicking on the beginning and end of the chain (marked with halos) you will see that the chain does not start at 1, nor does it end at 537. Notice that without examining the S2C listing, it would have been easy to overlook the missing residues in the crystallographic model.
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Appearance of a protein model that contains only alpha-carbon atoms (1A1D). |
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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.
Earlier versions of Firefox had problems with clicking on atoms to center or measure distances/angles. These problems are gone in Firefox 7.0.linux: Firefox appears to support FirstGlance in Jmol in Knoppix, but we have inadequate information for linux.
Problem with OS 10.3.9 only: In late 2005, the following problem occurs when using Safari under OS 10.3.9: Sometimes the links and buttons that control the molecular view fail to work. Simply quit and restart Safari to cure this problem, or upgrade to OS X 10.4 or later to avoid this problem entirely. The problem results when other java-using websites are visited before FirstGlance in Jmol in the same Safari session. The problem appears to reflect a bug in Apple's java. It has been reported to them.See also Mac Firefox and Compatible Browsers.
Another minor anomaly in Safari in OS 10.3.9 is that "hover" reports of atom identity do not appear. (They do appear in OS 10.4 and later.) However, in all versions of Safari/OS X, clicking an atom correctly produces an identity report in the lower left of the applet rectangle.
<form method='post' enctype='multipart/form-data' action='http://oca.weizmann.ac.il/oca-bin/fgij'> Upload a PDB file of your own: <br><small> Caution: uploading a PDB file may <b>disclose your data</b> to others. </small><br> <input type='file' name='file' size='50'> <input type='submit' value='View in FirstGlance'> </form>