help.js:	// Example: 1d66
help.js:	// Example: 1bl8
help.js:	// Example: 4mdh
help.js:	// Example: 1bl8 (none missing)
help.js:	// Examples: 4gxu, 1ucy (some of each).
help.js:	// Example: 2cyh
help.js:	// Example: 4ARF (due to swapping of CA and C in Gly2 of chain B)
help.js:	// Missing Example: 1d66
help.js:	// Blocked Example: none known yet.
help.js:	// Charged Example: 1bl8
help.js:	// Example: 1bl8 (none missing)
help.js:	// Example: 4ARF (due to swapping of CA and C in Gly2 of chain B)

help.js:Examples with incomplete sidechains include \
help.js:for nucleotides or nucleic acids. For example, examine the \n\
help.js:soluble proteins (examples: \n\
help.js:(examples:  \n\
help.js:'<br><br>Examples: \n\
help.js:'An example that has all three types of helices, <i>according to JSmol</i>, is \n\
help.js:In this example, 3<sub>10</sub> helices were specified by the authors in the PDB format \n\help.js:For example, the 4 chains in \
help.js:An example is the unusual triangular helix in  \n\
help.js:to work with such large models. (Example: 5leg.) \
help.js:'<br><b>Salt Bridge Examples</b> \n\
help.js:	hh += "<br><br>An example containing disulfide bonds (cystines), \
help.js:An example containing both interchain and intrachain disulfides is \
help.js:An example containing cysteines and no disulfide bonds is \
help.js:An example containing no cys residues is \
help.js:	hh += "<br><br>Examples: \
help.js:<a href="http://proteopedia.org/w/Temperature_color_schemes#Examples" \n\
help.js:target="_blank">Examples of crystallographic temperature values</a> at various \n\
help.js:<a href="http://proteopedia.org/w/Temperature_color_schemes#Examples" \n\
help.js:target="_blank">examples</a>). \n\

help1.js:	// EXAMPLES
help1.js:	occrep += "<br><br>Examples:<ul>" +
help1.js:'<li>See additional examples under ' +
help1.js:	erep += 'Examples with >10 elements: \
help1.js:<br>Examples with unknown elements Unx: \

help2.js:		if (pcount > pidcount) // Example?
help2.js:target="_blank">More examples</a>. \n\
help2.js:Examples: \n\
help2.js:Examples: \n\
help2.js:'When you touch or click on these atoms, you will see, for example, \n\
help2.js:For example, if \n\
help2.js:	<li>Atoms with alternate-location codes that nevertheless have only one location. Example
help2.js:<li>A more complicated example is \n\
help2.js:marked %C in this example. \n\
help2.js:<center><b>Examples</b></center><br> \n\
help2.js:A simple example is Glu3 in \n\
help2.js:target="_blank">3hyd</a>. In this example, the atom with the \n\
help2.js:Another example is  \n\
help2.js:<br><br>An unusual example is  \n\
help2.js:For example, \n\
help2.js:Another confusing example is  \n\
help2.js:'%. Protein examples are  \n\
help2.js:'%. Protein examples are \n\
help2.js:an example falling outside the appropriate range, please \n\
help2.js:For example, intrinsically disordered loops may have been held \n\
help2.js:Example 1: Some models have flexible <b>ends that protrude</b> from a \n\
help2.js:Examples are \n\
help2.js:Example 2: \n\
help2.js:Example 3: \n\
help2.js:portions of the asymmetric unit. Examples where this appears to \n\
help2.js:			' actual C-termini. Example: ' +
help2.js:	eeh += '<br>Examples:<ul>' +

help3.js:For example, the catalytic pocket of enolase (a glycolytic enzyme) \n\
help3.js:explains the example of Rett Syndrome. A detailed \n\
help3.js:Examples (simple): \n\
help3.js:Examples (well developed): \n\
help3.js:A classic example is  \n\
help3.js:to be solved crystallographically. Another example is porin, \n\

modeldat.js:but not excluding non-standard residues, for example
modeldat.js:			// Example chain C in 5fpk Met108A is missing, Ala108 has coordinates.
modeldat.js:// Phosphorylated 5' examples: 1evv
modeldat.js:			// Example: 4arc RNA chain B

moltab.js:// EXAMPLE NEEDED: CHAIN WITH NONE MISSING SEQID TO CHAIN WITH SOME MISSING.
moltab.js:// ABOVE EXAMPLES HAVE ONLY ONE MISSING SEGMENT PER CHAIN
moltab.js:// EXAMPLES:
moltab.js:// for EXAMPLES of PDB codes with various record counts etc.
moltab.js:// when a new name starts, no number again? (Need an example).
moltab.js:			// EXAMPLES ("REMARK 465" trimmed off by jgetfi())
moltab.js:// a good example for gapradius is 4b14
moltab.js:		// For example: 2.45 is rounded to 2.5 and used as 25.
moltab.js:// larger "host" chain. They may have charged N termini. See getNTHetero(), examples ther
moltab.js:	// CHARGE EXAMPLES:
moltab.js:	// HETERO CHARGE EXAMPLES HETERO - END EXAMPLES
moltab.js:		// NEED AN EXAMPLE OF A MISSING HET RESIDUE
moltab.js:	// See molvis/alternate locations with multiple models for dozens of examples.

scripts.js:// acids that are "not (protein,nucleic,hetero)". See examples in select.htm.
scripts.js:// See examples in versions.htm for version 2.5 under bugs fixed.
scripts.js:// AMINO ACIDS THAT LACK A BACKBONE ALPHA CARBON (no example known in PDB)
scripts.js:// Example: Gln8 in 4en3 lacks .n
scripts.js:// EXAMPLES TO DEEM AS CYCLIC NUCLEOTIDES:
scripts.js:// see list in cyclic_nucleotide_examples.txt
scripts.js:// EXAMPLES TO REPORT AS UNCHAINED NUCLEOTIDES BUT NOT "CYCLIC"
scripts.js:// EXAMPLES THAT SHOULD BE RECOGNIZED AS RNA BUT ARE NOT (JUST "LIGAND" NOW)
scripts.js:// residues (that are part of a chain) in spacefill. For example, 1EVV where
scripts.js:// (for example Gly in 4cpa and A in 1bkx)
scripts.js:// hetero (example?) but lack some backbone atoms.
scripts.js:// including N and C terminal charges. For example, 4cpa with its isolated single Glyci
scripts.js:		// (example: light chains Asp1 in 1igt), "and" with backbone.

bbinvis.htm:<b>Examples:</b> Adenosine A351:B is bound to protein in
bbinvis.htm:a backbone display. Another example is GLY1:G in
bbinvis.htm:such as the adenosine in the above example remains invisible with
bbinvis.htm:Example: in 1d66, the 5' ends of the DNA chains (C1:D and C20:E) lack
bbinvis.htm:An example of the use of "connected" is the following Jmol command.
bbinvis.htm:<big><b>Examples for Testing</b></big>
bbinvis.htm:Some published PDB file examples are described above under <i>The Problem</i>.
bbinvis.htm:An artificial set of examples was created by editing 1d66.pdb

biounit.htm:Interpret your results following the example below.
biounit.htm:<a name="buinterp"><b>Example Explaining Interpretation</b></a>
biounit.htm:as our example. The
biounit.htm:target="_blank">examples</a>
biounit.htm:<a href="http://proteopedia.org/w/Biological_Unit#Examples"
biounit.htm:target="_blank">a range of examples</a>.
biounit.htm:To try one of those examples, click on the PDB code. At the Proteopedia

endsmethods.htm:    sequence numbers. See examples in a new article I wrote recently: <a
endsmethods.htm:    However, I have stumbled across several examples with zero missing
endsmethods.htm:      even amino acids (e.g. acetyl, ACE). Examples: the N-terminal
endsmethods.htm:    <p>For example 3deq contains chain B of length 345 amino acids, 341
endsmethods.htm:    <p>Although I don't know of an example (and don't know how to search

issues.htm:<li> Displaying <b>alternative sidechain positions</b>. (Examples:
issues.htm:properly (see SV40 capid example in the
issues.htm:example, residues 1-3 in 
issues.htm:Dramatic examples are the TRP sidechains in the <i>Vines..</i> display in
issues.htm:<li>An example of a one-residue "chain"
issues.htm:that lacks a backbone-trace atom. An example is
issues.htm:<li>An example of a one-residue chain, visible because it is connected to

notes.htm:Examples:
notes.htm:labeled. Examples:
notes.htm:SEQCRD 0 S SER SER     4      4 C T 5         <b>EXAMPLE AT LEFT IS FOR 2ACE.</b>
notes.htm:<b>Examples</b> are
notes.htm:<a href="#nsr">non-standard residue</a> instead. An example
notes.htm:<b>Examples</b> include GLY308 in
notes.htm:An example is THR6 in
notes.htm:href="select.htm" target=_blank>examples</a>). Therefore,
notes.htm:Examples include the many non-standard nucleotides in the t-RNA
notes.htm:as HETATM. An example is
notes.htm:remediations. For example, SER or THR plus PHO became SEP or TPO in remediated
notes.htm:If you know of other cases not represented in the above examples,
notes.htm:Examples include
notes.htm:Examples include
notes.htm:Examples:
notes.htm:For example, you could enter a particular chain (prefix the chain name
notes.htm:	<b>Examples:</b>
notes.htm:with a second click. For example, if the selection mode is "Chains"
notes.htm:be deselected. For example:
notes.htm:see example below).
notes.htm:<br><li><b>Simple example of hydrogen bonds:</b>
notes.htm:<b>Example of non-bonds:</b> What appear to be hydrogen bonds in the "dry interface"
notes.htm:<br><b>Examples:</b>
notes.htm:example, between the two heavy chains in antibody
notes.htm:<br><b>Simple examples of hydrophobic interactions:</b>
notes.htm:<li><b>Example</b>: Each chain in <a href="fg.htm?mol=2hhd" target=_blank>2HHD</a> has one salt bridge
notes.htm:are in the same ring. An example is 
notes.htm:Examples include metal cations, or aromatic rings in ligands.
notes.htm:<b>Examples:</b>
notes.htm:The resulting set includes, for example, <b>O-metal, Se-metal,
notes.htm:The resulting set includes, for example, the sidechain <b>nitrogen
notes.htm:This includes, for example, <b>metal or chloride ions</b> interacting with
notes.htm:<ul><b>Examples (using <i>Contacts..</i>):</b>
notes.htm:<li><b>Example:</b> Select the single sodium ion in
notes.htm:The letter following a colon ("<b>:D</b>" in the example above)
notes.htm:<li>D amino acids. Examples:
notes.htm:<li>Ribothymidine. Example: 5MU in
notes.htm:<li>Deoxyribouridine. Example: DU in
notes.htm:<li>GLX or ASX (ambiguous) residues. Example:
notes.htm:<li>Unknown atoms X. Example:
notes.htm:<li>Unknown atoms or groups UNX or UNK. Examples:
notes.htm:<li>Unknown nucleotides "N". Examples:
notes.htm:<li>Unknown ligands "UNL". Examples:
notes.htm:<li><a href="#anomalous">Anomalous atoms</a>. Example: none known.
notes.htm:<li>Amino acids lacking alpha carbon atoms. Example: Thr918 in
notes.htm:<li>Amino acids lacking peptide-bonding atoms. Example: Gln8 in
notes.htm:<li>Amino acids lacking main chain oxygens. Examples: Gly5 in
notes.htm:<li>Single amino acid, not part of a polymer. Example: Gly308 in
notes.htm:Example: A351 in
notes.htm:Examples:
notes.htm:<li>Cyclic nucleotides. Examples:
notes.htm:<a href="cyclic_nucleotide_examples.txt"
notes.htm:target="_blank">Additional examples of cyclic nucleotides</a>.
notes.htm:<li>Alternate locations. Example: 3hyd. Atoms with alternate locations are haloed
notes.htm:Example:
notes.htm:Examples:
notes.htm:modeled with only backbone phosphorus atoms. Examples:
notes.htm:with coordinates (upon which to "hang" the empty baskts) were not found. Example:
notes.htm:conformers submitted in REMARK 210. Example: none known.
notes.htm:(Examples found earlier have been corrected by the PDB.)
notes.htm:<li>When there are multiple models with alternate locations. Example:
notes.htm:where a link reports the missing sequence numbers in each chain. Example:
notes.htm:Labeled with <b>S-</b> in the molecular display. Example:
notes.htm:atoms of each chemical element present. Example: 
notes.htm:and a link to <i>Find</i> alternate locations. Example:
notes.htm:Examples:
notes.htm:<b>Examples -- Odd PDB files now handled correctly</b>
notes.htm:Some example PDB codes are listed in the lower left help panel when you click <i>Ends</i>
notes.htm:Identification of chain ends is not perfect. For example, the end of chain F in

select.htm:This change seems desirable, though there is no example above where this
select.htm:One example is MYR1 and GLY1 in <b>1JSA</b> (see Note 2 above). Another

seqspecs.htm:share your ideas, suggestions, and additional juicy examples with
seqspecs.htm:	<li>See example below for 1QKZ:L.
seqspecs.htm:	<li>See example below for 1QKZ:L.
seqspecs.htm:	<li>See example below for 1QKZ:L.
seqspecs.htm:	<li>See example below for 1QKZ:L.
seqspecs.htm:For example, in 1CBN, residues
seqspecs.htm:<li>A checkbox to highlight <b>residues with missing atoms</b>. For example,
seqspecs.htm:	<li>(@@ examples needed)
seqspecs.htm:<b><big>C. Listing Examples</big></b>
seqspecs.htm:code A, is touched in the sequence listing for the example below, 1QKZ chain L:
seqspecs.htm:authors (see examples listed above). In the listing below,
seqspecs.htm:be numbered 1-30. In the example below, it includes residues numbered 1-27C
seqspecs.htm:For examples, see numbered items above on those topics.

versions.htm:"/fgij" in the URL. For example,
versions.htm:the structure. An extreme example with 48 &Aring; gaps is
versions.htm:Example:
versions.htm:Example:
versions.htm:<i>Chain Details</i> help. Its fairly amazing what you can find in there. Examples:
versions.htm:first conformation visible. For example, load
versions.htm:The first two <b>alternate conformations can be animated</b>. For example, load <b>2agt</b>
versions.htm:For example,
versions.htm:<li>An example has been provided that has multiple models and also atoms with alternate
versions.htm:target="_blank">OCA</a> for making it possible to find such examples.
versions.htm:when no sidechains are incomplete. Examples:
versions.htm:the situation and options. Examples:
versions.htm:<li><i>Ends</i> (<i>Tools</i> tab) has a new example. 1HVZ is a cyclic 18-amino acid. Both
versions.htm:Examples:
versions.htm:is an example having a C-terminal Lysine (chain B) with a missing sidechain; thus,
versions.htm:amino acid ligands (example
versions.htm:or dipeptide ligands (examples
versions.htm:for example the tripeptide in
versions.htm:that are not part of a chain. Examples: A351 in
versions.htm:in amino acids or nucleotides that are not part of a chain. Example: Gly308 in
versions.htm:<li>When a query that cannot be interpreted (example: >1) was entered in the <b>Find</b> dialog,
versions.htm:a molecule's URL</i>, the ready-made example was not working.
versions.htm:Examples of animated slides:
versions.htm:target="_blank">Examples and methods for <i>Find</i></a>
versions.htm:to show the counts of each. See examples under <i>Bugs Fixed</i> #27.
versions.htm:that the model is too large for the PDB format. Example:
versions.htm:under <i>Chain Details</i> (a link in the Molecule Information Tab). For example, the protein
versions.htm:<li>PDB files lacking headers were failing to load. Examples:
versions.htm:a header. See examples in the previous item.
versions.htm:in Jmol, kindly fixed by Bob Hanson. Example: <b>4o46</b>.
versions.htm:not shown in the example given there was between the main chain N of Thr198 and the carboxy
versions.htm:<li>Examples of animations saved from FirstGlance are provided:
versions.htm:When the model includes selenomethionine (MSE), a link is provided to an explanation. Example:
versions.htm:target="_blank">Gallery</a> under <i>ConSurf Examples</i>.
versions.htm:the target and contacting atoms were not being shown consistently. Example: in 1g9m, the covalent
versions.htm:<li>With certain large molecules (for example, 7ahl), in JSmol,
versions.htm:when the first operation was requested in FirstGlance (for example, toggle spinning off).
versions.htm:as balls. For example, 14 nucleotides contact the asymmetric unit of 1d66.
versions.htm:<a href="ppt/polyview-3d-examples.ppt"
versions.htm:For example, 1or9 is an 18-chain assembly. (Use Java for this large
versions.htm:produced a large spurious alert during loading. Example: 4fz0.
versions.htm:but with a new explanation and examples.
versions.htm:examples listed in the help.
versions.htm:to find them. Examples: 3hyd, 1bsz.
versions.htm:This makes it easier, for example,
versions.htm:An example is 4MDH (in
versions.htm:Examples:
versions.htm:residues. (Example:
versions.htm:<li>Added 1IGT (antibody) to the Gallery to provide an example with
versions.htm:Notes</a> were added to explain these definitions, and the examples of the
versions.htm:<a href="select.htm" target="selectwin">Examples</a>. Although the backbone
versions.htm:these parts of chains invisible. An example is 1AL4.
versions.htm:spheres. Examples with many inappropriately non-bonded atoms are

whatis.htm:Google Slides, Libre Office, etc.), or displayed in web pages such as the example at right.
whatis.htm:Here are more examples of animations from <i>FirstGlance</i>:
whatis.htm:target="_blank">Download Example Animations in Powerpoint</a>.
whatis.htm:target="_blank">View Example Animations Online in Google Slides</a>.
whatis.htm:Examples can be seen
whatis.htm:<li>Shows you <b>Crystal contacts</b> with examples of how they might affect the conformation
where.htm:<b>Anomalous atoms</b>: Atoms shown as dots in the initial view are "anomalous atoms" that do not fit the format standards for a Protein Data Bank data file. To hide these or change the rendering (or for examples), use Advanced/Technical in the Tools tab.
where.htm:<b>Disulfide bonds</b>: In the Tools tab. Highlights and counts disulfide bonds, as well as cysteines. Also counts sulfurs and selenium atoms, as well as methionines. Disulfide bonds are shown as thin yellow bars in the initial view, but may be difficult to see. In the Lower Left Panel help about disulfide bonds are listed many example PDB codes illustrating various cases.
where.htm:(example: <a href="fg.htm?mol=1lfa"
where.htm:(example: <a href="fg.htm?mol=2bbn"
where.htm:<b>Integral membrane protein</b>: To visualize hydrophobic surfaces of protein that may be buried in a lipid bilayer, see Hydrophobic/Polar in the Views tab. To visualize the predicted boundaries between lipid and polar environments, go to See Lipid Bilayer Boundaries in the Resources tab. Examples of membrane proteins are given in the help when you click Hydrophobic/Polar in the Views tab. 
where.htm:<b>Lipid bilayer boundaries</b>: To visualize hydrophobic surfaces of protein that may be buried in a lipid bilayer, see Hydrophobic/Polar in the Views tab. To visualize the predicted boundaries between lipid and polar environments, go to See Lipid Bilayer Boundaries in the Resources tab. Examples of membrane proteins are given in the help when you click Hydrophobic/Polar in the Views tab. 
where.htm:<b>Membrane protein</b>: To visualize hydrophobic surfaces of protein that may be buried in a lipid bilayer, see Hydrophobic/Polar in the Views tab. To visualize the predicted boundaries between lipid and polar environments, go to See Lipid Bilayer Boundaries in the Resources tab. Examples of membrane proteins are given in the help when you click Hydrophobic/Polar in the Views tab. 
where.htm:For an example, explore <b>1sjv</b>.
where.htm:as explained there. Note that you must prefix the sequence with "sequence=", for example, <b>sequence=TRFVIM</b> for a amino acids or <b>sequence=CGGAT</b> for DNA. 
where.htm:<b>Transmembrane protein</b>: To visualize hydrophobic surfaces of protein that may be buried in a lipid bilayer, see Hydrophobic/Polar in the Views tab. To visualize the predicted boundaries between lipid and polar environments, go to See Lipid Bilayer Boundaries in the Resources tab. Examples of membrane proteins are given in the help when you click Hydrophobic/Polar in the Views tab. 

0notes.txt:specified temperature range and give example of syntax.
0notes.txt:AU. Example where their absence is problematic: 1igt.
0notes.txt:select configuration=n for altlocs, see #49 in examples-11/new.htm
0notes.txt:Examples needed: long chain with multiple domains/hphob cores for polarity.
0notes.txt:the COMPND MOLECULE and SOURCE species. Example 1vu2.
0notes.txt:Example 4b14.
0notes.txt:Hydrophobic/polar: give examples of transmembrane and link OPM.
0notes.txt:Put 1k28.mmol on rcsb pdb directory for gallery. AND REPLACE EXAMPLE
0notes.txt:   the ConSurf example files work fine.
0notes.txt:Examples: 1a2b (GSP), 1r9s (UTP)
0notes.txt:Example: arg191 in 2kin.
0notes.txt:in Ppda, with examples, re uniform B factors, e.g. 2w54, see greenblatt's
0notes.txt:Good example: 2vpz polysulfide reductase has both phobic and philic in same
0notes.txt:A "hot link", for example:
0notes.txt:Could be added to bug examples, and anomalous docs.
charge.txt:getCharges() (moltab.js) has CHARGE EXAMPLES (search for that)
charge.txt:For HETERO END CHARGES, see moltab.js END EXAMPLES
cyclic_nucleotide_examples.txt:EXAMPLES OF CYCLIC NUCLEOTIDES
cyclic_nucleotide_examples.txt:EXAMPLES OF CYCLIC NUCLEOTIDES WITH CYCLIZED DIPHOSPHATES
ends.txt:Examples (for charge) in moltab.js at CHARGE EXAMPLES
ends.txt:For HETERO END CHARGES, see moltab.js END EXAMPLES
ends.txt:an example given in the manual under message, so 
find.txt:A good example of less technical is when "sequence=cgg" is found
insertio.txt:Examples: 1igt
ligand.txt:An example is ligand 3ES in 2xy9 which has a single alpha carbon, hence "protein".
ligand.txt:See CHARGE EXAMPLES in moltab.js.
memory.txt:http://chemapps.stolaf.edu/jmol/docs/examples-11/new8.htm
showpdb.txt:http://chemapps.stolaf.edu/jmol/docs/examples-11/new8.htm
showpdb.txt:Example:
showpdb.txt:modelInfo.models[0].file="http://chemapps.stolaf.edu/jmol/docs/examples-11/data/1d66.pdb"
state.txt:For example, SS bond Cys are not labeled by makeLabelSSBondsSpt()
viruses.txt:http://chemapps.stolaf.edu/jmol/docs/examples-11/new8.htm