Difference between revisions of "AtomSets"

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[http://nobinters.org/camini-e.htm camini e stufe] [http://nobinters.org/i-cavalieri.htm i cavalieri dello zodiaco] [http://nobinters.org/baby-can.htm baby can i hold you tonight] [http://davte.info/library/html/panini-spa.htm panini spa] [http://saibso.org/witch-hunter.htm witch hunter robin. vol. 05] [http://chaba.info/www-dolce/ www dolce e gabbana] [http://nobinters.org/affittacamere-lucca.htm affittacamere lucca] [http://ustall.org/web/lacafetera.htm lacafetera] [http://ustall.org/web/larva.htm larva] [http://kinunia.cn/gatitas.htm gatitas] [http://kinunia.cn/annunci-ragazze.htm annunci ragazze vogliose] [http://nobinters.org/fujifilm-finepix.htm fujifilm finepix f610] [http://nobinters.org/lupen-fisarmonica.htm lupen fisarmonica] [http://kinunia.cn/il-teatro.htm il teatro di john keats] [http://ashythro.info/library/html/celeron-d/ celeron d 336] [http://amohseni.info/img/styles/loewe-spheros/ loewe spheros 37 hd] [http://nobinters.org/www-finanze.htm www finanze] [http://ashythro.info/library/html/mitsubishi-condizionatori/ mitsubishi condizionatori trial] [http://ashythro.info/library/html/cavo-surround/ cavo surround] [http://helmed.info/topic/qvr-casio/ qv-r52 casio] [http://ustall.org/web/confort-trio.htm confort trio] [http://davte.info/library/html/firenze-zurigo.htm firenze zurigo biglietti aerei] [http://bloprofeldi.info/lib/centri-urbani.htm centri urbani] [http://psisemiya.com/images/small/de-bary/ de bary, heinrich anton] [http://davte.info/library/html/banconota-italiane.htm banconota italiane] [http://ashythro.info/library/html/nike-solas/ nike solas air] [http://davte.info/library/html/www-caravanbacci.htm www caravanbacci it] [http://chaba.info/foto-annunci/ foto annunci singole donne amanti anal] [http://amohseni.info/img/styles/amapola-com/ amapola com] [http://saibso.org/lettore-cd.htm lettore cd radio] [http://chaba.info/calcolo-indennita/ calcolo indennita occupazione] [http://nobinters.org/hyundai-p.htm hyundai 201p] [http://psisemiya.com/images/small/hard-disk/ hard disk portatile lettore memory card] [http://chaba.info/scuola-per/ scuola per estetista] [http://saibso.org/f.htm f410] [http://chaba.info/ever-/ ever 2005 q] [http://kinunia.cn/cd-britney.htm cd britney spears] [http://amohseni.info/img/styles/le-bouton/ le bouton d or] [http://helmed.info/topic/panasonic-lumix/ panasonic lumix 30] [http://saibso.org/virgilio-mail.htm virgilio mail] [http://chaba.info/ghost-norton/ ghost norton] [http://amohseni.info/img/styles/www-comune/ www comune di ardea it] [http://chaba.info/www-alpitur/ www alpitur com] [http://nobinters.org/cdv.htm cdv] [http://psisemiya.com/images/small/adattatori-prese/ adattatori prese corrente] [http://nobinters.org/uso-degli.htm uso degli automi cellulari] [http://davte.info/library/html/c-.htm c 50 zoom] [http://chaba.info/suzuki-ignis/ suzuki ignis] [http://helmed.info/topic/video-parishilton/ video parishilton] [http://saibso.org/dolls-kitano.htm dolls kitano] [http://saibso.org/www-impero.htm www impero romano it] [http://kinunia.cn/proietti-cavaliere.htm proietti cavaliere nero] [http://psisemiya.com/images/small/video-hard/ video hard gratuiti di oggi] [http://bloprofeldi.info/lib/ferrero-it.htm ferrero it] [http://bloprofeldi.info/lib/pentax-reflex.htm pentax reflex digitali] [http://nobinters.org/creare-libri.htm creare libri] [http://saibso.org/le-key.htm le key de tps france] [http://amohseni.info/img/styles/sorpassometro/ sorpassometro] [http://amohseni.info/img/styles/sony-sdm/ sony sdm 19] [http://amohseni.info/img/styles/de-pinguino/ de pinguino] [http://saibso.org/yacht-casio.htm yacht casio orologi] [http://kinunia.cn/lampade-al.htm lampade al neon] [http://ustall.org/web/gribingui.htm gribingui] [http://psisemiya.com/images/small/funkey/ funkey 256] [http://davte.info/library/html/dvd-a.htm dvd a hanging rock] [http://ustall.org/web/stampanti-inkjet.htm stampanti ink-jet a3 di rete] [http://ashythro.info/library/html/audio-esterna/ audio esterna accessori video] [http://ustall.org/web/shoshan-net.htm shoshan net] [http://nobinters.org/gp-player.htm gp player] [http://chaba.info/gadget-pubblicitari/ gadget pubblicitari] [http://saibso.org/pagine-personali.htm pagine personali travestiti] [http://davte.info/library/html/amd-athlon.htm amd athlon 64 desktop computer] [http://kinunia.cn/viet-michelle.htm viet michelle] [http://davte.info/library/html/batterie-sony.htm batterie sony np] [http://nobinters.org/case-esterno.htm case esterno hard disk 2 5] [http://davte.info/library/html/chill-out.htm chill out] [http://amohseni.info/img/styles/super-boby/ super boby world] [http://davte.info/library/html/decorazione-vetro.htm decorazione vetro sabbiatura] [http://davte.info/library/html/aiuta-babbo.htm aiuta babbo natale a] [http://saibso.org/danza-macabra.htm danza macabra] [http://psisemiya.com/images/small/micro-hifi/ micro hifi teac] [http://davte.info/library/html/meteo-web.htm meteo web] [http://davte.info/library/html/www-herbier.htm www herbier] [http://davte.info/library/html/ercis.htm ercis] [http://ustall.org/web/gioco-automobili.htm gioco automobili] [http://psisemiya.com/images/small/hotel-como/ hotel como ita] [http://psisemiya.com/images/small/black-eyed/ black eyed let] [http://psisemiya.com/images/small/bicchieri-pvc/ bicchieri pvc] [http://ustall.org/web/tre-passi.htm tre passi sulla terra] [http://chaba.info/joypad-playstation/ joypad playstation 2] [http://ustall.org/web/provini-veline.htm provini veline] [http://amohseni.info/img/styles/eleonora/ eleonora 86] [http://chaba.info/eizo-l/ eizo l550] [http://nobinters.org/platone-protagora.htm platone protagora] [http://helmed.info/topic/www-poltronesofa/ www poltronesofa it] [http://amohseni.info/img/styles/igor-sibaldi/ igor sibaldi] [http://bloprofeldi.info/lib/olympus.htm olympus 360] [http://saibso.org/televisore-plasma.htm televisore plasma lg 60] [http://chaba.info/bc-/ bc 20 canon] [http://bloprofeldi.info/lib/ragazze-in.htm ragazze in cam] [http://chaba.info/creare-e/ creare e stampare biglietti auguri] [http://bloprofeldi.info/lib/motorizazione-firenze.htm motorizazione firenze] [http://kinunia.cn/il-ratto.htm il ratto del serraglio] [http://saibso.org/porno-racconto.htm porno racconto] [http://bloprofeldi.info/lib/editto-di.htm editto di rotari] [http://chaba.info/dtt-/ dtt 4100 humax] [http://nobinters.org/gioca-jouer.htm gioca jouer midi] [http://bloprofeldi.info/lib/palmare-gps.htm palmare gps asus palmari] [http://saibso.org/immagini-o.htm immagini o foto del kamasutra] [http://bloprofeldi.info/lib/bruxelles-expo.htm bruxelles expo alberghi e hotel] [http://psisemiya.com/images/small/mini-moto/ mini moto cross] [http://saibso.org/kit-woofer.htm kit woofer] [http://ashythro.info/library/html/dvd-h/ dvd 2014h] [http://helmed.info/topic/mitchel-viet/ mitchel viet sex video] [http://saibso.org/ddr-sdram.htm ddr sdram 512] [http://davte.info/library/html/pc-spento.htm pc spento modem] [http://bloprofeldi.info/lib/sandra-the.htm sandra. the complete history] [http://chaba.info/origenes-del/ origenes del espiritismo] [http://chaba.info/juegos-manga/ juegos manga] [http://chaba.info/epson-a/ epson a3 ink] [http://bloprofeldi.info/lib/pane-e.htm pane e sale] [http://nobinters.org/voli-lamezia.htm voli lamezia terme] [http://davte.info/library/html/japanesegirls-com.htm japanesegirls com] [http://davte.info/library/html/profeti.htm profeti] [http://nobinters.org/i-need.htm i need your lovin] [http://psisemiya.com/images/small/gulasch/ gulasch] [http://davte.info/library/html/film-di.htm film di woody allen] [http://psisemiya.com/images/small/twista-overnight/ twista overnight celebrity] [http://psisemiya.com/images/small/pc-packard/ pc packard bell] [http://davte.info/library/html/stati-depressivi.htm stati depressivi nel bambino] [http://helmed.info/topic/batterie-nikon/ batterie nikon coolpix 5900] [http://psisemiya.com/images/small/nokia-/ nokia 8800 prezzo] [http://bloprofeldi.info/lib/acer-.htm acer - travelmate 630] [http://kinunia.cn/hotel-costa.htm hotel costa del sol] [http://bloprofeldi.info/lib/retribuzione-sufficiente.htm retribuzione sufficiente e condizioni locali] [http://kinunia.cn/rattan-arredo.htm rattan arredo giardino] [http://chaba.info/vecchio-renato/ vecchio renato zero] [http://nobinters.org/nina-badric.htm nina badric] [http://kinunia.cn/housekeeping.htm housekeeping] [http://ashythro.info/library/html/prete-fai/ prete, fai un miracolo] [http://chaba.info/no-me/ no me llames lola] [http://davte.info/library/html/racconti-.htm racconti  sculacciate] [http://psisemiya.com/images/small/finanziamento-potenza/ finanziamento potenza] [http://saibso.org/ufficio-friuli.htm ufficio friuli venezia giulia] [http://amohseni.info/img/styles/lavatrice-rex/ lavatrice rex incasso] [http://kinunia.cn/in-flash.htm in flash] [http://davte.info/library/html/rocky-mountain.htm 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[http://ashythro.info/library/html/mousse-t/ mousse t is it cause im cool] [http://nobinters.org/karaoke-cremonini.htm karaoke cremonini] [http://helmed.info/topic/lee-ryan/ lee ryan] [http://ustall.org/web/winmix-load.htm winmix load] [http://kinunia.cn/ragazza-san.htm ragazza san dona piave] [http://psisemiya.com/images/small/nino-d/ nino d angelo video] [http://bloprofeldi.info/lib/music-planet.htm music planet snc] [http://ustall.org/web/jolly-mask.htm jolly mask] [http://bloprofeldi.info/lib/caricaturas-de.htm caricaturas de amor] [http://psisemiya.com/images/small/sigma-/ sigma 70 300 obiettivi] [http://amohseni.info/img/styles/nikon-es/ nikon es e28] [http://bloprofeldi.info/lib/iomega-gb.htm iomega 60gb] [http://ashythro.info/library/html/aprile-a/ aprile a parigi] [http://amohseni.info/img/styles/shoshan-de/ shoshan de targets] [http://ashythro.info/library/html/barbecue-elettrica/ barbecue elettrica] [http://saibso.org/foto-di.htm foto di tutti i giornali americani] [http://amohseni.info/img/styles/asus-centrino/ asus centrino] [http://davte.info/library/html/gente-della.htm gente della notte] [http://davte.info/library/html/la-moglie.htm la moglie del soldato film dvd] [http://ustall.org/web/videocamera-mini.htm videocamera mini dv] [http://bloprofeldi.info/lib/aspire-.htm aspire 3002 lmi] [http://davte.info/library/html/la-vie.htm la vie zero] [http://amohseni.info/img/styles/incontri-salento/ incontri salento] [http://davte.info/library/html/la-spada.htm la spada del deserto] [http://nobinters.org/bomboniera-porcellana.htm bomboniera porcellana] [http://kinunia.cn/video-nothing.htm video nothing else matters dei metallica] [http://helmed.info/topic/super-duper/ super duper in love] [http://kinunia.cn/offerta-fotocamera.htm offerta fotocamera digitali] [http://ustall.org/web/seka-key.htm seka key] [http://chaba.info/saintgilles-belgio/ saint-gilles (belgio)] [http://ustall.org/web/hong-kong.htm hong kong 97] [http://psisemiya.com/images/small/pasticceria-calabrese/ pasticceria calabrese] [http://ustall.org/web/http-box.htm http box tim it mms] [http://saibso.org/kodak-camera.htm kodak camera dock] [http://amohseni.info/img/styles/sony-dscp/ sony dsc-p43] [http://bloprofeldi.info/lib/sfondi-samsung.htm sfondi samsung sghe700] [http://psisemiya.com/images/small/yale-linus/ yale, linus] [http://nobinters.org/caterina.htm caterina 883] {{Jmol_Documentation_Sections}}
 
= Predefined Atom Sets =
 
= Predefined Atom Sets =
  

Revision as of 07:15, 17 August 2007

camini e stufe i cavalieri dello zodiaco baby can i hold you tonight panini spa witch hunter robin. vol. 05 www dolce e gabbana affittacamere lucca lacafetera larva gatitas annunci ragazze vogliose fujifilm finepix f610 lupen fisarmonica il teatro di john keats celeron d 336 loewe spheros 37 hd www finanze mitsubishi condizionatori trial cavo surround qv-r52 casio confort trio firenze zurigo biglietti aerei centri urbani de bary, heinrich anton banconota italiane nike solas air www caravanbacci it foto annunci singole donne amanti anal amapola com lettore cd radio calcolo indennita occupazione hyundai 201p hard disk portatile lettore memory card scuola per estetista f410 ever 2005 q cd britney spears le bouton d or panasonic lumix 30 virgilio mail ghost norton www comune di ardea it www alpitur com cdv adattatori prese corrente uso degli automi cellulari c 50 zoom suzuki ignis video parishilton dolls kitano www impero romano it proietti cavaliere nero video hard gratuiti di oggi ferrero it pentax reflex digitali creare libri le key de tps france sorpassometro sony sdm 19 de pinguino yacht casio orologi lampade al neon gribingui funkey 256 dvd a hanging rock stampanti ink-jet a3 di rete audio esterna accessori video shoshan net gp player gadget pubblicitari pagine personali travestiti amd athlon 64 desktop computer viet michelle batterie sony np case esterno hard disk 2 5 chill out super boby world decorazione vetro sabbiatura aiuta babbo natale a danza macabra micro hifi teac meteo web www herbier ercis gioco automobili hotel como ita black eyed let bicchieri pvc tre passi sulla terra joypad playstation 2 provini veline eleonora 86 eizo l550 platone protagora www poltronesofa it igor sibaldi olympus 360 televisore plasma lg 60 bc 20 canon ragazze in cam creare e stampare biglietti auguri motorizazione firenze il ratto del serraglio porno racconto editto di rotari dtt 4100 humax gioca jouer midi palmare gps asus palmari immagini o foto del kamasutra bruxelles expo alberghi e hotel mini moto cross kit woofer dvd 2014h mitchel viet sex video ddr sdram 512 pc spento modem sandra. the complete history origenes del espiritismo juegos manga epson a3 ink pane e sale voli lamezia terme japanesegirls com profeti i need your lovin gulasch film di woody allen twista overnight celebrity pc packard bell stati depressivi nel bambino batterie nikon coolpix 5900 nokia 8800 prezzo acer - travelmate 630 hotel costa del sol retribuzione sufficiente e condizioni locali rattan arredo giardino vecchio renato zero nina badric housekeeping prete, fai un miracolo no me llames lola racconti sculacciate finanziamento potenza ufficio friuli venezia giulia lavatrice rex incasso in flash rocky mountain trophy hunter acquistare libro on line costantino vitigliano buona domenica sublimazione termica stampanti fotos de britney spears desnuda archos av420 20 gb www gemidos com ar hanging toner tn6600 p800 sony ericsson telefonia the economist satellite heaven ulka tagan u22 la oreja de van go drive motorola v 525 mousse t is it cause im cool karaoke cremonini lee ryan winmix load ragazza san dona piave nino d angelo video music planet snc jolly mask caricaturas de amor sigma 70 300 obiettivi nikon es e28 iomega 60gb aprile a parigi shoshan de targets barbecue elettrica foto di tutti i giornali americani asus centrino gente della notte la moglie del soldato film dvd videocamera mini dv aspire 3002 lmi la vie zero incontri salento la spada del deserto bomboniera porcellana video nothing else matters dei metallica super duper in love offerta fotocamera digitali seka key saint-gilles (belgio) hong kong 97 pasticceria calabrese http box tim it mms kodak camera dock sony dsc-p43 sfondi samsung sghe700 yale, linus caterina 883

Jmol + JSmol Documentation

Predefined Atom Sets

Jmol recognizes and uses several keywords or tokens for several purposes: commands in the scripting language, colors, etc. Among them, there are keywords for predefined atom sets:

By element name:

carbon, oxygen, hydrogen, sulphur, etc.

On Jmol 11, element symbol preceded by underscore can also be used: _C, _O, _H, _S, etc. Also, deuterium or _D, and tritium or _T.

On PDB format, Jmol will identify the element from columns 77-78 (element symbol, right-justified). If this is absent, then it will interpret the "atom name" field (columns 13-14) to deduce the element identity.

Note: Jmol 10.2 has a bug by which it may read calcium as alpha carbon based on its ID, although identification by element name works properly. It's been fixed for Jmol 11.

By type of molecule:

  • amino:
This is based only upon group name and has nothing to do with the actual atoms that make up the group.
This set is composed of all groups with one of these names: ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ASX, GLX, UNK.
This will usually be the 20 canonical proteinogenic amino acids, plus ambiguous Asp/Asn (ASX), ambiguous Glu/Gln (GLX) and 'unknown' (UNK).
  • protein:
The 'protein' set in Jmol is based solely on the atoms that make up the group. It is independent of the group name and independent of whether the atoms are defined in ATOM records or HETATM records.
This has the advantage that modified groups and interesting things that are not amino acids can still be identified as part of the protein.
The atoms that make up the set are recognized by the names of the atoms.
  • Case 1:
If the group has 4 atoms named N, CA, C and (O or O1) and they are bonded in the correct order, then the group is considered protein.
  • Case 2:
If the group has exactly 1 atom whose name is CA then it is considered protein. The purpose of this is to pick up alpha-carbon-only models
  • nucleic:
A group is considered 'nucleic' if it contains atoms with all of these names: C3*, O3*, O5*, N1, C2, N3, C4, C5, C6 (asterisk may be substituted by prime/apostrophe). It is independent of the group name and independent of whether the atoms are defined in ATOM records or HETATM records.
  • rna:
A group is 'rna' if it is 'nucleic' and it also contains an atom named O2* (or O2').
  • dna:
A group is 'dna' if it is 'nucleic' and it does not contain an atom named O2* (or O2').
  • water:
This set is composed of groups named HOH, DOD, or WAT.
  • ions:
This set is composed of groups named PO4 or SO4.
  • solvent:
water or ions.
  • ligand:
hetero and not solvent (needs confirmation; at least, it is so in Rasmol)

By type of residue:

Inclusion in this sets is determined by residue id (only as far as it is written in the adequate field in the molecular coordinate file, usually PDB format).

Residue IDs:

  • Nucleotides: A, G, C, T, U
  • Amino acids: the 3-letter standard abbreviation

Residue sets:

  • Nucleotides: purine, pyrimidine, at, cg
  • Amino acids:
    • acyclic, cyclic, aliphatic, aromatic
    • large (Arg,Glu,Gln,His,Ile,Leu,Lys,Met,Phe,Trp,Tyr), medium (Asn,Asp,Cys,Pro,Thr,Val), small (Ala,Gly,Ser)
    • polar, nonpolar, hydrophobic (Ala,Gly,Ile,Leu,Met,Phe,Pro,Trp,Tyr,Val), neutral, charged, acidic, negative, basic, positive, ...
    • buried (Ala,Cys,Ile,Leu,Met,Phe,Trp,Val), surface
  • hetero, ions, ligand, water, solvent (see above)

By structure of the polymer:

  • helix, sheet, turn
  • bonded

Parts in proteins:

Backbone or Mainchain

Inclusion in this set is determined by atom id*, as follows:

  • Peptide bond: N, H (bound to N), CA (alpha carbon), HA (bound to CA), C (carbonyl carbon), O or O1 (bound to C)
  • In glycine, the two equivalent hydrogens are both in the backbone set: either H1 and 1HA or 1HA and 2HA.
  • Termini:
    • second carbonyl oxygen on C-terminus: OXT
    • terminal amino hydrogens: 1H, 2H, 3H

(*)Note: on PDB format: atom id is called atom name, and must be in these positions/columns:

  • 13-14 : Chemical symbol, right justified, except for hydrogen atoms
  • 15 : Remoteness indicator (alphabetic); e.g., in amino acid residues, alpha = A, beta = B, gamma = G, delta = D, epsilon = E.
  • 16 : Branch designator (numeric).

Sidechain

Defined as (not backbone).

Alpha

A set defined by atom id CA.

Parts in nucleic acids:

Backbone or Mainchain

Inclusion in this set is determined by atom id*, as follows:

  • Phosphate groups:
    • phosphorus: P
    • oxygens bound to phosphorus: O1P, O2P
  • Atoms in pentose:
    • carbon ring: C1', C2', C3', C4', C5'
    • hydrogens attached to carbon ring: H1', 1H2', 2H2' (only DNA), H3', H4', 1H5' and 2H5'
    • hydroxyls: O2', O3', O4', O5', 2HO' (H on 2'-hydroxyl, only RNA) (the ring oxygen is denoted O4, not O1).

Note: PDB files label pentose atoms with asterisk instead of prime signs. How does Jmol cope with this? Not much of a trouble: given the asterisk is a wildcard, "select C3*" will get pentose carbons either labeled with prime or asterisk!.

  • Termini:
    • 5'-terminus oxygen (no phosphate): O5T
    • 5'-terminus hydrogen (attached to O5T or O5'): H5T
    • 3'-terminus hydrogen (on 3'-hydroxyl): H3T
  • Atoms in bases:
    • ring, both purines and pyrimidines: N1, C2, N3, C4, C5, C6
    • ring, purines: N7, C8, N9
    • ring, pyrimidines: O2
    • substituents on ring:
      • in cytosine: N4
      • in guanine: N2
      • in adenine: N6
      • in thymine: C5M
      • in guanine and hypoxanthine: O6
      • in thymine and uracil: O4
      • in thiouracil: S4

(*)Note: on PDB format, atom id is called atom name, and must be in these positions/columns:

  • 13-14 : Chemical symbol, right justified, except for hydrogen atoms
  • 15 : Remoteness indicator (alphabetic).
  • 16 : Branch designator (numeric).

Sidechain

Defined as (not backbone).

Bases

Synonim of (nucleic and sidechain).

User-defined Atom Sets

A set can be created, and assigned any group of atoms, by giving it a name, using

define whatever_name atom_expression

Later, that set's name can be used as the predefined ones, in commands select, restrict, show, hide, etc.