View source for Missing residues and incomplete sidechains

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Most [[empirical models]] are missing standard amino acid or nucleotide residues that were present in the experimental material, and/or sidechain atoms, and therefore are often missing charges present in the intact molecule. These missing parts make errors in the shape of the molecule as well as the distribution of charges, hydrophobic and polar regions, and often there are missing [[salt bridges]] and [[cation-pi interactions]]. [[FirstGlance in Jmol]] makes it less likely, compared to other popular viewers, to overlook missing parts. '''[[AlphaFold| AlphaFold models]], which lack no atoms (other than hydrogen), should be analyzed alongside empirical models in order to see complete structures.'''
==Missing Residues==
In about 80%<ref name="oca">Percentages are based on searches for REMARK 465 and REMARK 470 at [https://oca.weizmann.ac.il/oca-bin/ocamain OCA], and searches for ''unobserved residues'' and ''unobserved atoms'' at [https://rcsb.org RCSB].</ref> of the [[Empirical models]] in the [[PDB]], some residues (amino acids or nucleotides) that were present in the experimental material are absent (have no coordinates) in the empirical model. The breakdown by method as of February, 2025:
* 83% of X-ray crystallography entries have missing residues.
* 14% of solution NMR entries have missing residues.
* 93% of electron microscopy entries have missing residues.

[[X-ray crystallography]] gives a clear electron density map only where every molecule in the protein crystal has the same conformation. Usually, some parts of the molecule vary in conformation between copies in the crystal, that is, some regions are '''disordered'''.  The same may occur with protein molecules on a [[cryo-electron microscopy]] grid. These disordered portions of the molecule are not clearly resolved in the density map used to construct the structure model. Without density to guide where to place these residues, the experimenter omits them from the model. These are called ''missing residues''. It is very common for a few residues at the ends of protein [[chains]] to be missing in the atomic model. ({{font color|#c000c0|Example: 5 residues are missing from the carboxy terminus of the protein in [[1ijw]].}}) In addition to disorder rendering residues "invisible", residues can actually be lost by proteolysis during purification, or radiation damage during [[X-ray crystallography]] can sometimes remove atoms<ref name="damage">PMID: 10639129</ref>, and conformations can be affected by crystallization conditions<ref name="methyleneblue">PMID: 26990888</ref>.

To emphasize, in most cases, the missing residues were believed to be '''present''' in the experimental material, but are '''absent''' in the resulting atomic model. ''Missing residues'' are distinct from ''intentionally deleted residues'' that were not present in the experimental material due to engineering of the cloned 
and expressed protein.

===Get The Best Model Available===

Before you spend time working with an empirical model, make sure you have chosen the highest resolution and most complete model available. [[How_To_Find_A_Structure#Sequence-Related_Empirical_Models|Search for sequence-identical (or nearly identical) models]]. For a step by step guide, see [[How to find a protein's best structure]]. Things will be much easier if the sequence numbers in the empirical model are the same as the UniProt numbering. If not, consider [[Renumbering PDB files|renumbering the PDB file]].

===Missing Ends of Chains===

Unlike other viewers, [[FirstGlance in Jmol]] ensures that you are aware of missing ends by marking them with  spherical "empty baskets". In the example shown below, [[2ace]], the 3 missing N-terminal residues DDH have net negative charge.

<table class="wikitable" style="text-align:center;"><tr><th colspan=5>
[[2ace]] amino-terminus missing 3 amino acids
</th><th>
[https://www.uniprot.org/uniprotkb/P04058/entry P04058] AlphaFold:<br>None Missing
</th></tr><tr><td>
[[Image:2ace-fg-missing-nterm.png]]
</td><td>
[[Image:2ace-pymol-missing-nterm.png|105px]]
</td><td>
[[Image:2ace-chimerax-missing-nterm.png|128px]]
</td><td>
[[Image:2ace-molstar-missing-nterm.png|128px]]
</td><td>
[[Image:2ace-icn3d-missing-nterm.png|110px]]
</td><td>
[[Image:AF-P04058-nterm-extended.png|100px]]
</td></tr><tr><td width=150>
[[FirstGlance]] "empty basket".
</td><td>
[[PyMOL]]
</td><td>
[[ChimeraX]]
</td><td>
[[Molstar]]
</td><td>
[[iCn3D]]
</td><td>
[[FirstGlance]]
</td></tr></table>

===Missing Loops===

[[FirstGlance]] ensures that you are aware of missing loops with an ellipsoidal "empty basket". Other viewers use a  dotted line, which is easier to overlook when viewing the entire structure. Empty baskets are easily hidden<ref name="hiding">See [https://proteopedia.org/wiki/fgij/where.htm#h Hiding empty baskets].</ref>.

<table class="wikitable" style="text-align:center;"><tr><th colspan=5>
[[2ace]] missing 5 amino acid loop
</th><th>
[https://www.uniprot.org/uniprotkb/P04058/entry P04058] AlphaFold:<br>None Missing
</th></tr><tr><td>
[[Image:2ace-fg-missing-loop.png|160px]]
</td><td>
[[Image:2ace-pymol-missing-loop.png|154px]]
</td><td>
[[Image:2ace-chimerax-missing-loop.png|170px]]
</td><td>
[[Image:2ace-molstar-missing-loop.png|170px]]
</td><td>
[[Image:2ace-icn3d-missing-loop.png|160px]]
</td><td>
[[Image:AF-P04058-loop.png|130px]]
</td></tr><tr><td width=150>
[[FirstGlance]] "empty basket" (see [[#below]])<ref name="sminus-nterm">The "S-" indicates that Lys491 has an incomplete sidechain, extending only to the gamma carbon.</ref>
</td><td>
[[PyMOL]]
</td><td>
[[ChimeraX]]
</td><td>
[[Molstar]]
</td><td>
[[iCn3D]]
</td><td>
[[FirstGlance]]
</td></tr></table>

===See For Yourself===

* [http://firstglance.jmol.org/fg.htm?mol=2ace 2ace in FirstGlance in Jmol]
* [https://www.rcsb.org/3d-view/2ACE/1 2ace in Mol*]
* [https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbid=2ace&bu=1 2ace in iCn3D]
* ([[PyMOL]] and [[ChimeraX]] require that you download stand-alone applications.)

===AlphaFold models have no missing atoms===
When all [[empirical models]] of the protein of interest have missing atoms, the best way to get a model without missing atoms is to [https://alphafold.ebi.ac.uk download the AlphaFold model]. The downloaded PDB file can then be uploaded to [http://firstglance.jmol.org FirstGlance]. [https://www.ncbi.nlm.nih.gov/Structure/icn3d/ iCn3D] will accept the UniProt sequence ID to retrieve the AlphaFold model directly.

Models from the AlphaFold Database are limited to '''single-chain''' structures without ligands, but starting in 2024, see [[How to predict structures with AlphaFold]] for servers that can predict '''multiple-chain''' structures (protein, DNA, RNA) with ligands or modified residues.

The AlphaFold model will usually be nearly identical to the [[empirical model]] (''you should verify this by [[How_To_Find_A_Structure#Structure_Superposition|superposition]]''), but will include the missing residues/atoms. Structures of missing loops will be predicted by AlphaFold, but typically with lower confidence ([https://proteopedia.org/wiki/index.php/AlphaFold_pLDDT_and_expected_distance_error lower pLDDT]) than the remainder of the structure. Many long loops that are missing in empirical models are actually [[Intrinsically_Disordered_Protein|intrinsically disordered]], in which case those loops predicted by AlphaFold will have very low confidence and be meaningless.

===Why Missing Residues Matter===

Where residues are completely missing in [[empirical models]], the shape of the molecule will be incorrect, and when charged residues are missing, the distribution of charges will be incorrect, as well as the distribution of hydrophobic and polar patches. [[Salt bridges]] and [[cation-pi interactions]] may be missing.

====Example: [[5nyp]]====

{{font color|#c000c0|[[5nyp]] is a bacterial protein believed to be an ancestor of the 20S proteasome<ref name="5nyp">PMID: 29355501</ref>.}} ''All sequence numbers given below are UniProt numbering. Subtract one to match numbering in 5nyp.''
*[[5nyp]] has '''3 missing loops''', clustered on one face. Their lengths are 8, 10, and 12 residues (20-27, 102-111, 183-194).
*None of the 3 missing loops are predicted to be [[Intrinsically Disordered Protein|intrinsically disordered]] by [[RCSB]]<ref name="iupred">PMID: 32237272</ref>. The first missing loop is predicted to be disordered by [http://biomine.cs.vcu.edu/servers/flDPnn2/ flDPnn2]<ref name="fldpnn">PMID: 39237195</ref>. The other two are not. But flDPnn2a predicts disorder for 71-83, which is not missing.
*The missing loops include '''7 charged amino acids''' (4&ndash;, 3+).
*Although the authors did not detect proteolytic activity with the substrates tested, the putative '''catalytic triad''' residues Thr2, Asp18, and Lys33 (UniProt numbers) are '''present'''.
*When present in the AlphaFold model, two of the '''missing loops partially obscure the putative catalytic triad'''.
*'''Two salt bridges are missing''' in 5nyp that are present in the AlphaFold model. UniProt Glu107 (present) forms a salt bridge with missing Arg99. UniProt Asp183 forms a salt bridge with arg187 -- both are missing in 5nyp.

<table class="wikitable"><tr><th colspan=3>
Three Missing Loops in [[5nyp]]. Snapshots from [[FirstGlance]].
</th></tr><tr><td width="300">
[[Image:5nyp-rainbow-fgij.png|300px]]
</td><td width="300">
[[Image:5nyp-catres-adj-missing-noendbasket.png|300px]]
</td><td width="300">
[[Image:AF-F8JB59-fgij.png|300px]]
</td></tr><tr><td>
[[5nyp]]: missing loops (in front) as ellipsoidal "empty baskets"<ref name="bluesphere">There is a spherical blue "empty basket" on the amino terminus because Met1 is missing. This spherical empty basket was removed in the image showing the putative catalytic triad.</ref>. {{Template:ColorKey_N2CRainbow}}
</td><td>
[[5nyp]]: yellow halos on putative catalytic triad, showing proximity to missing loops (in front).
</td><td>
AlphaFold-predicted structure for [https://www.uniprot.org/uniprotkb/F8JB59/entry F8JB59]. Loops missing in [[5nyp]] are '''at top'''.
Confidence (>70 is "confident"): [[Image:PLDDT-color-key-fgij.png|300px]]
</td></tr></table>

=====AlphaFold Prediction Superposed on [[5nyp]]=====

<table class="wikitable"><tr><td rowspan=3>
The three missing loops are present in the [[AlphaFold]] prediction for [https://www.uniprot.org/uniprotkb/F8JB59/entry UniProt F8JB59]. [[How_To_Find_A_Structure#Structure_Superposition|FATCAT]] superposed the AlphaFold prediction onto all 213 alpha carbons of [[5nyp]] with [[RMSD]] 2.4 &Aring;. The FATCAT-generated [[morph]] between the two models shows their similarity. Their similarity shows that the AlphaFold model is largely correct.
</td><th>
'''{{font color|#a09040|AlphaFold Prediction}}''' Superposed on '''{{font color|#4090e0|5nyp}}'''
</th><th width="350">
[[Morph]] Between Models
</th></tr><tr><td width="350">
[[Image:5nyp-AF-fatcat-superposition.png|350px]]
</td><td>
[[Image:Morph-5nyp-af-cut2.gif]]
</td></tr><tr><td><center>
Missing loops at top.
</center></td><td><center>
[http://firstglance.jmol.org/videocapture.htm Captured] from [[How_To_Find_A_Structure#Structure_Superposition|FATCAT]].
</center></td></tr></table>

=====Missing Loops Obstruct Catalytic Site=====

<table class="wikitable"><tr><td rowspan=3>
Missing loops affect the shape of the molecule. The putative catalytic site is exposed on [[5nyp]], but when the 3 loops are added in [[AlphaFold]]'s prediction for [https://www.uniprot.org/uniprotkb/F8JB59/entry UniProt F8JB59], they partially obstruct the putative catalytic site.
</td><th>
[[5nyp]]
</th><th width="350">
AlphaFold-Predicted Structure
</th></tr><tr><td width="350">
[[Image:5nyp-charge-catres.gif]]
</td><td>
[[Image:AF-F8JB59-charge-catres-loops.gif]]
</td></tr><tr><td colspan=2><center>
Charged atoms colored by [[FirstGlance]]<ref name="fgcharge" />: {{font color|blue|Positive +}}, {{font color|red|Negative &ndash;}}.
Putative catalytic triad: <span class="bg-yellow">yellow halos</span>.
Loops predicted by AlphaFold in dark gray.
</center></td></tr></table>

=====Missing Charges in [[5nyp]]=====

<table class="wikitable"><tr><td rowspan=3>
The three missing loops include 4 negatively-charged amino acids, and 3 positively charged ones.
Their absence affects the distribution of charge on the surface, as shown in these [[electrostatic potential maps]] generated by [[iCn3D]] (from a link in the Views tab in [[FirstGlance]]).
</td><th width="350">
[[5nyp]]: 3 loops with 7 charges are missing.
</th><th width="350">
AlphaFold-Predicted Structure for [https://www.uniprot.org/uniprotkb/F8JB59/entry F8JB59]: No missing charges.
</th></tr><tr><td width="350">
[[Image:5nyp-epm-icn3d.png|350px]]
</td><td>
[[Image:AF-F8JB59-epm-icn3d.png|350px]]
</td></tr><tr><td colspan=2><center>
Electrostatic potential maps by [[iCn3D]] (from a link in the Views tab of [[FirstGlance]]):
<br>
{{font color|blue|Positive +}}, {{font color|red|Negative &ndash;}}.
</center></td></tr></table>

=====Missing Salt Bridges in [[5nyp]]=====

<table class="wikitable"><tr><td rowspan=3 width="500">
Two salt bridges are missing in [[5nyp]] as a result of two of the missing loops.
At left: Missing UniProt Glu107 forms a salt bridge with Arg99 (present).
At right: UniProt Asp183 forms a salt bridge with Arg187 -- both are missing in [[5nyp]].
A salt bridge also forms between two of the putative catalytic triad residues, Lys31 and Asp169.
(All 3 triad residues are present in [[5nyp]].)
</td><th width="400">
AlphaFold-Predicted Structure for [https://www.uniprot.org/uniprotkb/F8JB59/entry F8JB59].
</th></tr><tr><td width="350">
[[Image:5nyp-catres-vs-AF-F8JB59-sb.png|400px]]
</td></tr><tr><td><center>
Salt bridges rendered by [[FirstGlance]]<ref name="fgsb">To display and list all salt bridges in a protein, click ''Salt Bridges'' in the ''Tools'' tab.</ref>:
{{font color|blue|Positive +}}, {{font color|red|Negative &ndash;}}.
<span class="bg-yellow">Yellow halos</span>: Charges missing in [[5nyp]].
<span class="bg-lightgreen">Green halos</span>: Putative catalytic triad, present in [[5nyp]].
'''Black backbone''': loops missing in [[5nyp]].
</center></td></tr></table>

==Incomplete Sidechains==
In about half<ref name="oca" /> of the [[Empirical models]] in the [[PDB]], some residues have coordinates missing for some of their sidechain atoms, due to local disorder. But their main chain atoms are present in the model; thus, they are residues with ''incomplete sidechains''. For example, the long sidechain of a lysine on the surface of a protein may have too blurry an electron density to indicate its position. In some cases, the model builder may give that sidechain coordinates with high [[temperature]]s, or low or zero [[occupancy]] ({{font color|#c000c0|example: Arg321 in [[2ade]]}}<ref name="2ade">In [[2ade]], the temperature of the distal nitrogens in Arg321 is 79, while the average temperature is 31.</ref>). In other cases, the model builder simply omits the coordinates for the sidechain, so the aforementioned surface lysine may have the sidechain of an alanine ({{font color|#c000c0|example: Lys498 in [[2ace]]}}).

Among the five viewers shown below, only FirstGlance alerts you to incomplete sidechains in its initial view. It marks them '''S&mdash;'''. FirstGlance and iCn3D are the only ones that show disulfide bonds in their initial views, although, as you can see in the snapshots below, [[Introduction_to_molecular_visualization#Disulfide_Bonds|FirstGlance makes them more obvious]]. The '''S&mdash;''' labels are easily hidden when desired<ref>See [http://firstglance.jmol.org/notes.htm#labels Labels on Atoms: S&mdash;, X, D, ?].</ref>.

<table class="wikitable" style="text-align:center;"><tr><th colspan=5>
Initial views of incomplete sidechains in [[2ace]]
</th></tr><tr><td>
[[Image:2ace-s-minus-fgij.png|250px]]
</td><td>
[[Image:2ace-s-minus-pymol.png|250px]]
</td><td>
[[Image:2ace-s-minus-chimerax.png|250px]]
</td><td>
[[Image:2ace-s-minus-molstar.png|250px]]
</td><td>
[[Image:2ace-s-minus-icn3d.png|250px]]
</td></tr><tr><td width=150>
[[FirstGlance]] marks incomplete sidechains with '''S&mdash;''', and shows disulfide bonds.
</td><td>
[[PyMOL]]
</td><td>
[[ChimeraX]]
</td><td>
[[Molstar]]
</td><td>
[[iCn3D]] shows disulfide bonds.
</td></tr></table>

===Do incomplete sidechains matter?===

Obviously, incomplete sidechains matter when they occur near a region of interest in an [[empirical model]]. The easiest way to get a model without incomplete sidechains is to use the AlphaFold model, bearing in mind that residue positions and sidechain rotamer orientations may be inexact.

====Atoms colored by charge====

When the charged atoms are missing in incomplete sidechains, there is '''little effect''' when spacefilling atoms are colored by charge in FirstGlance or iCn3D, because they '''color the entire residue''' by charge. [[FirstGlance]] initially colors only charged '''atoms'''. Where the charged sidechain atoms are missing, [[FirstGlance]] colors the remainder of the residue in a lighter color, with a checkbox option to color all atoms in charged residues, as does iCn3D.

<table class="wikitable" style="text-align:center;"><tr><th colspan=4>
Atoms Colored By Charge: [[2ace]] With Incomplete Sidechains,
{{font color|blue|Positive +}}, {{font color|red|Negative &ndash;}}
</th></tr><tr><td>
[[Image:2ace-orientation.png|220px]]
</td><td width="250">
[[Image:2ace-fg-charged-atoms.png|250px]]
</td><td>
[[Image:2ace-fg-charged-residues.png|250px]]
</td><td>
[[Image:2ace-icn3d-charge.png|250px]]
</td></tr><tr><td width=150>
[[FirstGlance]]: orientation for all snapshots.
</td><td>
[[FirstGlance]] default<ref name="fgcharge">To color a protein by charge in FirstGlance, click ''Charge'' in the ''Views'' tab.</ref>: charged '''atoms''', light colors for incomplete sidechains.
</td><td>
[[FirstGlance]] charged '''residues''' checked.
</td><td>
[[iCn3D]]<ref name="icn3dcharge">To color a protein by charge in iCn3D: Style, Protein, Spheres; then Color, Charge.</ref>
</td></tr></table>
(No "single button" to color spacefilling atoms by charge was evident in Molstar or ChimeraX. In ChimeraX, the commands to do this can be saved as a "preset".)

====Surface colored by electrostatic potential====

When either ChimeraX or iCn3D color a surface by [[electrostatic potential maps|electrostatic potential]], incomplete sidechains affect the map. Therefore, it is '''critical to use the AlphaFold-predicted structure''' that has neither missing residues nor incomplete sidechains. 

<table class="wikitable" style="text-align:center;"><tr><th colspan=4>
Surface Colored By Electrostatic Potential vs. Incomplete Sidechains for [[2ace]],
{{font color|blue|Positive +}}, {{font color|red|Negative &ndash;}}
</th></tr><tr><td width="100">
[[ChimeraX]]<ref name="cxepm">To generate an electrostatic potential map in ChimeraX, with nothing selected, click ''electrostatic'' in the ''Molecule Display'' tab. To intensify the colors, reduce the default range (-10 to 10), for example to -5 to 5, select the desired protein, then enter this command: ''coulombic sel range -5,5''.</ref>
</td><td width="250">
[[Image:2ace-epm-chimerax.png|250px]]
</td><td width="250">
[[Image:2ace-epm-chimerax-sidechains-complete.png|250px]]
</td><td width="250">
[[Image:AF-P04058-22-558-epm-chimerax-800px.jpg|250px]]
</td></tr><tr><td>
[[iCn3D]]<ref name="max6">Electrostatic potential maps were created in iCn3D using its Analysis, Delphi Potential, Surface with potential, with default settings except the max potential was set to 6 kT/e.</ref>
</td><td>
[[Image:2ace-icn3d-max6.png|250px]]
</td><td>
[[Image:2ace-epm-icn3d-sicechains-complete.png|250px]]
</td><td>
[[Image:AF-P04058-22-558-icn3d.png|250px]]
</td></tr><tr><td>
Structure Visualized
</td><td>
[[2ace]] with incomplete sidechains.
</td><td>
[[2ace]] with all sidechains complete.<ref name="deepview">To fill in incomplete sidechains in [[2ace]], the PDB file was loaded into [[Swiss-PDBViewer]], then saved. It completes sidechains automatically. It does NOT fill in missing residues.</ref>
</td><td>
AlphaFold-predicted structure for [https://www.uniprot.org/uniprotkb/P04058/entry P04058], with both ends trimmed.<ref name="trimmed">The ends absent from the protein crystallized for [[2ace]] were deleted using a [[Plain text editor]]. The signal sequence 1-21 was deleted from the N terminus. The C terminus starting with 559 was deleted; it is a tetramerization domain (see next reference).</ref><ref name="tetramerization">PMID: 15526038</ref>.
</td></tr><tr><td colspan=4><center>
Orientations for all snapshots are the same as in the previous table.
</center></td></tr></table>

==How to avoid overlooking missing residues or incomplete sidechains==

Regions with '''missing residues''' are clearly marked with "empty baskets" when a PDB ID model is displayed in [http://firstglance.jmol.org FirstGlance in Jmol], as shown above. FirstGlance reports the total number missing, and the resulting number of missing charges. And it offers a detailed report (see snapshot below), which also lists all the missing residues (from PDB file REMARK 465).

FirstGlance also marks '''incomplete sidechains''' with '''S&ndash;''', and (when you opt to ''Show More Details'') provides a count of Incomplete Sidechains (see snapshot below). Clicking ''Find/List'' at that count enables you to list all the residues with incomplete sidechains.

{{font color|magenta|Example in FirstGlance [[4ifd]]:}} (When there are >100 incomplete sidechains, the S&ndash; labels are initially suppressed to reduce clutter.)
<br>
[[Image:Fgij-4ifd-missingres.jpg|1000px|border]]

==Missing residues and atoms lists in PDB and mmCIF files==
===PDB Format===
Quoting from the legacy [https://files.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v32_A4.pdf PDB Format Description]:
<blockquote>
"<b>REMARK 465</b> lists the residues that are <b>present in the SEQRES</b> records but are completely
<b>absent from the coordinates section</b>."
</blockquote>
SEQRES lists only protein and nucleic acid linear polymer residues, not carbohydrate or other residues of [[hetero atoms]]. Therefore, missing residues of polysaccharides or other HETERO compounds are not listed in the PDB file.

Similarly,
<blockquote>
"<b>REMARK 470</b>: <b>Non-hydrogen atoms of standard residues</b> which are missing from the coordinates are listed.
<b>Missing HETATMs</b> (atoms within hetetrogen groups) are <b>not listed</b> here."
</blockquote>

Example:
*Look for REMARK 465 and REMARK 470 in the [https://files.rcsb.org/view/2ACE.pdb PDB file for 2ACE].
*Look for empty baskets and S&mdash; labels for [http://firstglance.jmol.org/fg.htm?mol=2ace 2ACE in FirstGlance].

====Zero occupancy vs. missing atoms====

Atoms with zero occupancy have coordinates, and therefore are not listed as missing. For example, [[1nsa]] (1997, resolution 2.3 &Aring;) has 64 distal sidechain atoms with zero occupancy on the surface of the protein.
[[3dxx]] (2009, resolution 2.1 &Aring;) has 27 distal surface sidechain atoms with zero occupancy.
Neither has REMARK 470.
Additional zero occupancy cases are [[8pch]] and [[3b1d]].
Alternatively, these atoms could have been left missing (giving [[#Incomplete_Sidechains|incomplete sidechains]]), a more typical treatment of weak electron densities.

[[FirstGlance in Jmol]] tabulates a summary of occupancies, and can list partial occupancies in spreadsheet-ready form, for example 
*[http://firstglance.jmol.org/fg.htm?mol=1nsa 1NSA in FirstGlance]: Click <font color='red'>Show More Details</font>, then scroll down in the upper left panel to click ''Occupancy''.

===mmCIF Format===

[https://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html PDB to PDBx/mmCIF Data Item Correspondences] provides <b>no</b> information about REMARK 465 or REMARK 470.

Although <tt>[https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_missing_residue_list.html pdbx_missing_residue_list]</tt> and <tt>[https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_missing_atom_poly.html _pdbx_missing_atom_poly]</tt> are in the mmCIF dictionary, they are described as <b>not used in current PDB entries</b>.

It appears that these lists are in <tt>[https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_unobs_or_zero_occ_residues.html pdbx_unobs_or_zero_occ_residues]</tt> and <tt>[https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_unobs_or_zero_occ_atoms.html pdbx_unobs_or_zero_occ_atoms]</tt>. However, these mmCIF categories lump together missing (unobserved) and zero occupancy cases, unlike the separation of these two categories in the PDB format.

Examination of mmCIF files suggests that missing residues are also indicated by "?" in certain data items of category <tt>[https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_poly_seq_scheme.html _pdbx_poly_seq_scheme]</tt>.

==Incomplete Sidechain Repair==

If you need to add the missing atoms for incomplete sidechains without changing the positions (coordinates) for any existing atoms, here are two methods:

* Use the free [https://www.protein-science.com Protein Repair & Analysis Server].
* Simply load the PDB file into free [https://spdbv.unil.ch/ Swiss PDB Viewer], then save it. This program automatically adds missing sidechain atoms. However, the program will not run on Mac OS 10.15 or higher. It will not run on Silicon CPU Macs.

==See Also==
*[[Unusual sequence numbering]]

==Notes & References==
<references />