Selection Issues in Jmol Command Scripts
with Proposals for Improvements to Jmol

Problems selecting ligands+, non-standard residues, and protein are indicated in red.
Results in black are OK.
Results below are for Jmol 10.2.0.

- Most problems in the columns below Displayed as ... in FGiJ have been corrected in the FGiJ displays by "exception handling" modifications to the command scripts (scripts.js. see also notes.htm). It is anticipated that these exception handling modifications could be removed after Jmol has been upgraded to deal with the problems documented below.
- The results of these workarounds in FG are indicated below in brown.
- Jmol's handling of some unusual situations is deemed acceptable.

PDB Code | Group Name or Atom | =(protein,nucleic) | Chain | Hetero | Ligand | Displayed as Ligands+ in FGiJ | Displayed as NSR* in FGiJ
2BBN (no NSR*) | Ca | YES | A | Yes | Yes | Yes | No
1TCO | Ca FE, ZN, PO4, MYR, FK5: OK | YES | (none) | Yes | Yes | Yes | No
1EVV | NSR* Mg, SPM | Yes No | A (none) | Yes Yes | Yes Yes | No Yes | Yes No
1H3O | THR918.N (lacks all other atoms) MSE | No Yes | A A | No Yes | No Yes | Yes No | No Yes
1LCD (no NSR*) | Na | No | (none) | Yes | Yes | Yes | No
1K28 | K PO4 MSE | No No Yes | (none) (none) Yes | Yes Yes Yes | Yes No** Yes | Yes Yes No | No No Yes
310D | Mg CH3 | No No | (none) Yes | Yes Yes | Yes Yes | Yes Yes | No No
1B07 | GLY5 (notes 1,3) lacks =O on .C PYL | NO No | C C | No Yes | No Yes | No Yes | No No
1AL4 | VAL1,ILE1^A,GLY2,ALA3 (note 3) DLE, DVA (see bugsjmol.htm) FOR POL | NO Yes No No | A,B A,B A,B (none) | No Yes Yes Yes | No Yes Yes Yes | No No Yes Yes | No Yes No No
1UC5 | MET79:M K, NH4, PGR, CNC: OK | NO | M | No | No | No | No
1JSA | MYR1 (note 2) | YES | (none) | No | No | NO | YES
2SOC | CYS, PHE, LYS, THR (note 3) DPN, DTR, THO | NO Yes | (none) (none) | No Yes | No Yes | No No | No Yes
1GRH | CYS (note 3) HEC | NO No | (none) (none) | No Yes | No Yes | No Yes | No No
1PRC | ALA333.N:C (lacks all other atoms) FOR0:H ("ATOM"! error in PDB) see 1PRC below | No No | C H | No No | No No | No No | No No

* NSR = Non-Standard Residues (amino acids or nucleotides)
**Solvent includes PO4 in 1K28.

Note 1: Standard residues that are in ATOM records, yet not deemed protein by Jmol sometimes lack atoms:

- THR918 in 1H3O lacks all atoms except N! (REMARK 470) The 2 N's can be selected as "not (protein,hetero)".
- GLY5:C in 1B07 lacks O (REMARK 470). GLU2, VAL3, ARG11 (all chain C) lack sidechain atoms (REMARK 470) but are deemed protein.
- VAL1 etc. in 1AL4 appears intact (N, CA, C, O, sidechain) ???
- MET79:M in 1UC5 lacks O (REMARK 470)

Note 2: 1JSA's single unnamed chain begins with MYR1 (HETATM) then GLY1 (ATOM). Jmol incorrectly deems the MYR1 to be protein. "select myr" selects the glycine atoms as well. "select myr not hetero" selects only the glycine atoms. "select myr and gly" selects 0.

Note 3: FG shows these with dots as "anomalous atoms". See notes.htm#anomalous

Other test PDB's:

- 1EHZ is like 1EVV with many hydrated Mo ligands, and many nonstandard residues. OK in FGiJ.
- 1NEK: 2 Ca's, not in a chain, are deemed protein as in 1TCO in the table. Similarly for 1JSA.
- 1PRC: ALA333:C deemed nonprotein, missing atoms not in REMARK 470; lots of other ligands OK in FGiJ.
- 1C4S: ASG, GCU (carbohydrate, some sulfated) and Na; no protein. OK in FGiJ.
- 1IGT: GAL, MAN, FUC, NAG protein glycosylation. OK in FGiJ.
- 1C8R: LI1, SQU, RET OK in FGiJ.
- 1AOI: nucleosome, lots of DNA and protein; no NSR. Mn's display as ligand. OK in FGiJ.
- 1EMB: (GFP), CRO is handled as ligand. OK in FGiJ.
- 1VCX: All water is DOD. Jmol correctly selects it as water, and colors the deuterium "other", not white.

Preamble to proposals for changes in Jmol

RasMol and Chime divide all atoms into ATOM (protein,nucleic) or HETATM (hetero). Hetero is further sub-divided into solvent (water/HOH, DOD, and inorganic sulfate and phosphate) with all non-solvent being subsumed in the term "ligand". No HETATM can be protein or nucleic. All atoms are either (protein,nucleic) or hetero; no atoms are neither.

In Jmol, (protein,nucleic) is allowed to include HETATM's that meet certain criteria. This enables hetero non-standard residues (NSR) to be included in backbone traces, and excluded from "ligand", which is desirable. It also allows the selection of NSR with "(hetero and (protein,nucleic))" [when the authors of the PDB file have designated the entire NSR as HETATM, as in 1BKX, but not when the main-chain portions are designated ATOM, as in 1APM]. Being able to distinguish NSR from ligand is desirable.

In some PDB files, Jmol deems some "orphan" atoms neither (protein,nucleic) nor hetero, notably standard amino acids that lack the usual atoms (1TCO). This seems acceptable, since such atoms can be detected by selecting "not (protein,nucleic,hetero)".

See further discussion in notes.htm#nsr

Proposals for changes in Jmol:

1. If something is (protein,nucleic), it cannot also be ligand. (As stated in the preamble above, in RasMol and Chime, these are mutually exclusive, which seems a good thing.) This change removes NSR from ligand, enabling us to exclude ligand from the NSR display. This change seems desirable, though there is no example above where this is crucial (but only because I have not used the term ligand in selections in FGiJ). In FG, NSR are selected with "(protein,nucleic) and hetero"; ligand with "not (protein,nucleic,water)".
2. Any atom that belongs to an ATOM (not HETATM) group with one of the standard amino acid or nucleotide names should be (protein,nucleic), unless it lacks main chain atoms. (It would be PDB-format-illegal for atoms to have a standard residue name and be HETATM.) This change corrects the present failure to deem standard residues as protein in 1B07 and 1UC5. [The reason why VAL1 in 1AL4, and 4 standard amino acids in 2SOC, and CYS in 1GRH are deemed nonprotein is unclear to me. None have missing main-chain atoms.] As stated elsewhere in this document, the fact that THR918.N in 1H3O lacks all atoms except .N is reason enough for Jmol not to deem these .N's "protein".
3. It may be necessary to permit two distinct residues in the same chain to have the same number, yet different characteristics. One example is MYR1 and GLY1 in 1JSA (see Note 2 above). Another is 1DPO, which has two different amino acids at positions 184, 188, and 221 without insertion codes. This is probably very rare, and might be illegal in PDB format?
4. 918.N in 1H3O is reported to be oxygen by CPK color, and in the hover report (not shown in table above). This bug needs to be corrected.

It would be more appropriate to display the CH3 in 310D and the PYL in 1B07 as NSR (rather than ligand), but this is probably difficult to achieve, and we can live with the present situation.