Difference between revisions of "AtomSets"

From Jmol
Jump to navigation Jump to search
m
(ammending definition of "solvent" to include "ions")
 
(20 intermediate revisions by 4 users not shown)
Line 1: Line 1:
[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 rocky mountain trophy hunter] [http://bloprofeldi.info/lib/acquistare-libro.htm acquistare libro on line] [http://bloprofeldi.info/lib/costantino-vitigliano.htm costantino vitigliano buona domenica] [http://kinunia.cn/sublimazione-termica.htm sublimazione termica stampanti] [http://psisemiya.com/images/small/fotos-de/ fotos de britney spears desnuda] [http://psisemiya.com/images/small/archos-av/ archos av420 20 gb] [http://ustall.org/web/www-gemidos.htm www gemidos com ar] [http://kinunia.cn/hanging.htm hanging] [http://ustall.org/web/toner-tn.htm toner tn6600] [http://nobinters.org/p-sony.htm p800 sony ericsson telefonia] [http://amohseni.info/img/styles/the-economist/ the economist] [http://nobinters.org/satellite-heaven.htm satellite heaven] [http://amohseni.info/img/styles/ulka/ ulka] [http://psisemiya.com/images/small/tagan-u/ tagan u22] [http://psisemiya.com/images/small/la-oreja/ la oreja de van go] [http://amohseni.info/img/styles/drive-motorola/ drive motorola v 525] [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}}
+
{{Jmol_Documentation_Sections}}
 
= Predefined Atom Sets =
 
= 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:
+
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: ==
+
Please note that many of these keywords only apply to file formats that specify a residue ID or group ID as part of the information for each atom (most typically, <code>pdb</code> and <code>mmcif</code> formats, designed for macromolecules).
 +
 
 +
:''Technical note'': most of these are set in [http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/viewer/JmolConstants.java?view=markup src/org/jmol/viewer/JmolConstants.java]
 +
 
 +
== By element name ==
 
<tt>carbon</tt>, <tt>oxygen</tt>, <tt>hydrogen</tt>, <tt>sulphur</tt>, etc.
 
<tt>carbon</tt>, <tt>oxygen</tt>, <tt>hydrogen</tt>, <tt>sulphur</tt>, etc.
  
Line 13: Line 17:
 
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.
 
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: ==
+
== By type of element ==
* <tt>amino</tt>:
+
:''(new in Jmol 14.6)''
 +
* <tt>nonMetal</tt>: H; B; C, Si; N, P, As; O, S, Se, Te; F, Cl, Br, I, At; noble gases
 +
* <tt>metal</tt>: all except <tt>nonMetal</tt>
 +
* <tt>metalloid</tt>: B, Si, Ge, As, Sb, Te ''(note it overlaps with both metal and metalloid)''
 +
* <tt>alkaliMetal</tt>: from Li down to Fr
 +
* <tt>alkalineEarth</tt>: from Be down to Ra
 +
* <tt>nobleGas</tt> from He down to Rn
 +
* <tt>transitionMetal</tt>: from Sc to Zn, from Y to Cd, from Hf to Hg, from Rf to Cn
 +
* <tt>lanthanide</tt>: La, from Ce to Lu
 +
* <tt>actinide</tt>: Ac, from Th to Lr
 +
 
 +
== By type of molecule ==
 +
* <tt>amino</tt>
 
: This is based only upon group name and has nothing to do with the actual atoms that make up the group.
 
: 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 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).
 
: This will usually be the 20 canonical proteinogenic amino acids, plus ambiguous Asp/Asn (ASX), ambiguous Glu/Gln (GLX) and 'unknown' (UNK).
  
* <tt>protein</tt>:
+
* <tt>protein</tt>
 
: 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.
 
: 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.
 
: This has the advantage that modified groups and interesting things that are not amino acids can still be identified as part of the protein.
Line 28: Line 44:
 
:: 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
 
:: 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
  
* <tt>nucleic</tt>:
+
* <tt>peptide</tt>
 +
: The 'peptide' set in Jmol matches a 'protein' that has between 2 and 12 residues.
 +
:: only Jmol 14.29.1 or later
 +
:: defined as <code>protein and within(chain,monomer>1) and not within(chain,monomer>12)</code>
 +
 
 +
* <tt>nucleic</tt>
 
: 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.
 
: 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.
  
* <tt>rna</tt>:
+
* <tt>rna</tt>
: A group is 'rna' if it is 'nucleic' and it also contains an atom named O2* (or O2').
+
: A group is 'rna' if it is <tt>nucleic</tt> and it also contains an atom named O2* (or O2').
 +
 
 +
* <tt>dna</tt>
 +
: A group is 'dna' if it is <tt>nucleic</tt> and it '''does not''' contain an atom named O2* (or O2').
  
* <tt>dna</tt>:
+
* <tt>carbohydrate</tt>
: A group is 'dna' if it is 'nucleic' and it '''does not''' contain an atom named O2* (or O2').
+
: This is based only upon group name.
 +
: This set is composed of all groups which name is in a (not comprehensive) list corresponding to common mono-, di- and trisaccharides ([[AtomSets/Carbohydrate|full list and identities]]).
  
* <tt>water</tt>:
+
* <tt>water</tt>
: This set is composed of groups named HOH, DOD, or WAT.
+
: Any molecule chemically interpreted as water (an oxygen atom connected to two hydrogen, deuterium or tritium atoms), plus groups named HOH, DOD, or WAT.
 +
:: The original implementation of this set was only the named groups.
  
* <tt>ions</tt>:
+
* <tt>ions</tt>
: This set is composed of groups named PO4 or SO4.
+
: This set is not what might seem, but it's just composed of groups named PO4 or SO4.
 +
:: ''Explanation'': Both are common ions in protein crystals for X-ray diffraction, and this special set (which is RasMol syntax) is kept for backward compatibility.
  
* <tt>solvent</tt>:
+
* <tt>solvent</tt>
: <tt>water</tt> or <tt>ions</tt>.
+
: This includes <tt>water</tt> (in its extended definition), UREA groups and also <tt>ions</tt> (PO4 and SO4 by their residue/group name in the pdb file).
  
* <tt>ligand</tt>:
+
* <tt>ligand</tt>
: <tt>hetero</tt> and not <tt>solvent</tt> (needs confirmation; at least, it is so in Rasmol)
+
:: ''Note: <code>ligand</code> will, in some occasions, '''not''' match what you expect.''
 +
: The new definition (Jmol 12.2) includes atoms that do not belong to protein, nucleic or water. As a consequence,
 +
:* <tt>ions</tt> and <tt>carbohydrate</tt> '''are''' considered <code>ligands</code>.
 +
:* <tt>water</tt> is '''not''' considered <code>ligands</code>.
 +
:* Nonstandard amino acids are '''''not''''' considered <code>ligands</code>.
 +
:* Nonstandard nucleotides are '''''not''''' considered <code>ligands</code>.
 +
:* Isolated nucleotides (e.g. ATP, GTP, AMP...) are '''''not''''' considered <code>ligands</code> (despite being understood by us as ligands; this is due to them being part of the <code>nucleic</code> atom set). To account for this, you may choose to use <code>polymer=0 and not water</code> instead of <code>ligand</code> ''(this works only in most recent versions like 14.3.12)''
 +
: Ligand was clasically defined as <tt>hetero</tt> and not <tt>solvent</tt> (and so not always what you would expect from the word ligand, either).
  
== By type of residue: ==
+
== 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).
+
Inclusion in these sets is mostly determined by residue id (only as far as it is written in the adequate field in the molecular coordinate file, usually PDB format). A few cases are also included based on their chemical structure and the presence of a distinguishing atom name.
  
 
Residue IDs:
 
Residue IDs:
* Nucleotides: <tt>A, G, C, T, U</tt>
+
* Nucleotides: <tt>A, G, C, T, U, DA, DG, DC, DT</tt> but also based on their chemical <tt>nucleic</tt> structure and certain atom names. <tt>tu</tt> gets thiouridine.
 
* Amino acids: the 3-letter standard abbreviation  
 
* Amino acids: the 3-letter standard abbreviation  
  
Line 63: Line 97:
 
** <tt>polar, nonpolar, hydrophobic (Ala,Gly,Ile,Leu,Met,Phe,Pro,Trp,Tyr,Val), neutral, charged, acidic, negative, basic, positive,</tt> ...
 
** <tt>polar, nonpolar, hydrophobic (Ala,Gly,Ile,Leu,Met,Phe,Pro,Trp,Tyr,Val), neutral, charged, acidic, negative, basic, positive,</tt> ...
 
** <tt>buried (Ala,Cys,Ile,Leu,Met,Phe,Trp,Val), surface</tt>
 
** <tt>buried (Ala,Cys,Ile,Leu,Met,Phe,Trp,Val), surface</tt>
* <tt>hetero, ions, ligand, water, solvent</tt> (see above)
+
* <tt>hetero, carbohydrate, ions, ligand, water, solvent</tt> (see above)
  
== By structure of the polymer: ==
+
== By structure of the polymer ==
 
* <tt>helix, sheet, turn</tt>
 
* <tt>helix, sheet, turn</tt>
 
* <tt>bonded</tt>
 
* <tt>bonded</tt>
  
== Parts in proteins: ==
+
== Parts in proteins ==
 
=== <tt>Backbone</tt> or <tt>Mainchain</tt> ===
 
=== <tt>Backbone</tt> or <tt>Mainchain</tt> ===
 
Inclusion in this set is determined by '''atom id'''*, as follows:
 
Inclusion in this set is determined by '''atom id'''*, as follows:
Line 81: Line 115:
  
 
(*)Note: on PDB format: '''atom id''' is called ''atom name'', and must be in these positions/columns:
 
(*)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
+
:* 13-14 : Chemical symbol, right justified, except for hydrogen atoms
* 15 : Remoteness indicator (alphabetic); e.g., in amino acid residues, alpha = <tt>A</tt>, beta = <tt>B</tt>, gamma = <tt>G</tt>, delta = <tt>D</tt>, epsilon = <tt>E</tt>.
+
:* 15 : Remoteness indicator (alphabetic); e.g., in amino acid residues, alpha = <tt>A</tt>, beta = <tt>B</tt>, gamma = <tt>G</tt>, delta = <tt>D</tt>, epsilon = <tt>E</tt>.
* 16 : Branch designator (numeric).
+
:* 16 : Branch designator (numeric).
  
 
=== <tt>Sidechain</tt> ===
 
=== <tt>Sidechain</tt> ===
Line 91: Line 125:
 
A set defined by '''atom id''' <tt>CA</tt>.  
 
A set defined by '''atom id''' <tt>CA</tt>.  
  
== Parts in nucleic acids: ==
+
== Parts in nucleic acids ==
 
=== <tt>Backbone</tt> or <tt>Mainchain</tt> ===
 
=== <tt>Backbone</tt> or <tt>Mainchain</tt> ===
 
Inclusion in this set is determined by '''atom id'''*, as follows:
 
Inclusion in this set is determined by '''atom id'''*, as follows:
Line 103: Line 137:
 
** hydrogens attached to carbon ring: <tt>H1', 1H2', 2H2'</tt> (only DNA), <tt>H3', H4', 1H5'</tt> and <tt>2H5'</tt>
 
** hydrogens attached to carbon ring: <tt>H1', 1H2', 2H2'</tt> (only DNA), <tt>H3', H4', 1H5'</tt> and <tt>2H5'</tt>
 
** hydroxyls: <tt>O2', O3', O4', O5', 2HO'</tt> (H on 2'-hydroxyl, only RNA) (the ring oxygen is denoted <tt>O4</tt>, not <tt>O1</tt>).
 
** hydroxyls: <tt>O2', O3', O4', O5', 2HO'</tt> (H on 2'-hydroxyl, only RNA) (the ring oxygen is denoted <tt>O4</tt>, not <tt>O1</tt>).
 
+
: Note: old 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, "<tt>select C3*</tt>" will get pentose carbons either labeled with prime or asterisk!.
<blockquote>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, "<tt>select C3*</tt>" will get pentose carbons either labeled with prime or asterisk!.
 
</blockquote>
 
  
 
* Termini:
 
* Termini:
Line 112: Line 144:
 
** 3'-terminus hydrogen (on 3'-hydroxyl): <tt>H3T</tt>
 
** 3'-terminus hydrogen (on 3'-hydroxyl): <tt>H3T</tt>
  
* Atoms in bases:
+
* Atoms in bases (excluded from <tt>backbone</tt>):
 
** ring, both purines and pyrimidines: <tt>N1, C2, N3, C4, C5, C6</tt>
 
** ring, both purines and pyrimidines: <tt>N1, C2, N3, C4, C5, C6</tt>
 
** ring, purines: <tt>N7, C8, N9</tt>
 
** ring, purines: <tt>N7, C8, N9</tt>
Line 126: Line 158:
  
 
(*)Note: on PDB format, '''atom id''' is called ''atom name'', and must be in these positions/columns:
 
(*)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
+
:* 13-14 : Chemical symbol, right justified, except for hydrogen atoms
* 15 : Remoteness indicator (alphabetic).
+
:* 15 : Remoteness indicator (alphabetic).
* 16 : Branch designator (numeric).
+
:* 16 : Branch designator (numeric).
  
 
=== Sidechain ===
 
=== Sidechain ===
Line 134: Line 166:
  
 
=== Bases ===
 
=== Bases ===
Synonim of <tt>(nucleic and sidechain)</tt>.
+
Synonym of <tt>(nucleic and sidechain)</tt>.
  
 
= User-defined Atom Sets =
 
= User-defined Atom Sets =
 
A set can be created, and assigned any group of atoms, by giving it a name, using
 
A set can be created, and assigned any group of atoms, by giving it a name, using
 
  '''define''' ''whatever_name'' ''atom_expression''
 
  '''define''' ''whatever_name'' ''atom_expression''
Later, that set's name can be used as the predefined ones, in commands <code>select, restrict, show, hide</code>, etc.
+
Later, that set's name can be used as the predefined ones, in commands <code>select, restrict, display, hide</code>, etc.
 +
 
 +
You can also use [{{ScriptingDoc}}#jmolmath JmolScript variables] for this purpose.
 +
 
 +
= Selecting atom sets from the pop-up menu =
 +
See [[AtomSets/Popup Menu]].

Latest revision as of 19:26, 6 September 2023

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.

Please note that many of these keywords only apply to file formats that specify a residue ID or group ID as part of the information for each atom (most typically, pdb and mmcif formats, designed for macromolecules).

Technical note: most of these are set in src/org/jmol/viewer/JmolConstants.java

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 element

(new in Jmol 14.6)
  • nonMetal: H; B; C, Si; N, P, As; O, S, Se, Te; F, Cl, Br, I, At; noble gases
  • metal: all except nonMetal
  • metalloid: B, Si, Ge, As, Sb, Te (note it overlaps with both metal and metalloid)
  • alkaliMetal: from Li down to Fr
  • alkalineEarth: from Be down to Ra
  • nobleGas from He down to Rn
  • transitionMetal: from Sc to Zn, from Y to Cd, from Hf to Hg, from Rf to Cn
  • lanthanide: La, from Ce to Lu
  • actinide: Ac, from Th to Lr

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
  • peptide
The 'peptide' set in Jmol matches a 'protein' that has between 2 and 12 residues.
only Jmol 14.29.1 or later
defined as protein and within(chain,monomer>1) and not within(chain,monomer>12)
  • 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').
  • carbohydrate
This is based only upon group name.
This set is composed of all groups which name is in a (not comprehensive) list corresponding to common mono-, di- and trisaccharides (full list and identities).
  • water
Any molecule chemically interpreted as water (an oxygen atom connected to two hydrogen, deuterium or tritium atoms), plus groups named HOH, DOD, or WAT.
The original implementation of this set was only the named groups.
  • ions
This set is not what might seem, but it's just composed of groups named PO4 or SO4.
Explanation: Both are common ions in protein crystals for X-ray diffraction, and this special set (which is RasMol syntax) is kept for backward compatibility.
  • solvent
This includes water (in its extended definition), UREA groups and also ions (PO4 and SO4 by their residue/group name in the pdb file).
  • ligand
Note: ligand will, in some occasions, not match what you expect.
The new definition (Jmol 12.2) includes atoms that do not belong to protein, nucleic or water. As a consequence,
  • ions and carbohydrate are considered ligands.
  • water is not considered ligands.
  • Nonstandard amino acids are not considered ligands.
  • Nonstandard nucleotides are not considered ligands.
  • Isolated nucleotides (e.g. ATP, GTP, AMP...) are not considered ligands (despite being understood by us as ligands; this is due to them being part of the nucleic atom set). To account for this, you may choose to use polymer=0 and not water instead of ligand (this works only in most recent versions like 14.3.12)
Ligand was clasically defined as hetero and not solvent (and so not always what you would expect from the word ligand, either).

By type of residue

Inclusion in these sets is mostly determined by residue id (only as far as it is written in the adequate field in the molecular coordinate file, usually PDB format). A few cases are also included based on their chemical structure and the presence of a distinguishing atom name.

Residue IDs:

  • Nucleotides: A, G, C, T, U, DA, DG, DC, DT but also based on their chemical nucleic structure and certain atom names. tu gets thiouridine.
  • 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, carbohydrate, 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: old 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 (excluded from backbone):
    • 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

Synonym 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, display, hide, etc.

You can also use JmolScript variables for this purpose.

Selecting atom sets from the pop-up menu

See AtomSets/Popup Menu.