Seqtool: Difference between revisions

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The purpose of this tool is to make it easy to relate sequence to 3D structure within any Proteopedia page. By design the listing is kept simple. Sequence annotations such as secondary structure or sequence motifs can be viewed in other databases, and need not be shown here.

=== Description ===

=== Description of sequence display ===

Whenever a model is loaded into JSmol, a sequence listing is displayed for each chain. Chain is picked from a drop-down menu. If the model has a single chain, it will be displayed by default.

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Both ribonucleotides and deoxyribonucleotides in nucleic acids are converted to single-letter.

~~'''Sequence~~ to ~~3D'''~~

The sequence includes a combination of:

* Residues with atoms that have coordinates (ATOM records in the file) and are also included in SEQRES records; these are displayed as uppercase letters.

* Residues that lack coordinates but are mentioned in SEQRES records in the file (i.e. a physical gap, typically due to crystallographic disorder); these are displayed as lowercase letters; the reported residue number is an estimation, correlative to the adjacent residue with coordinates (an interpolated number is desirable but not currently implemented).

* Residues inferred due to a numbering gap (absent from both SEQRES and ATOM records) are displayed as the number of missing residues surrounded by tilde (~) signs.

* Residues in ATOM records that are absent in SEQRES records reflect sequence microheterogeneity; the alternate residues at the same sequence position are enclosed in square brackets.

* Inserted residues are listed in-line with other residues, but displayed as superscript letters.

~~'''Hovering''' the pointer over a one-letter code displays, above the sequence, the full ID of the residue and, in the case of hetero groups, its description.~~

=== Interaction ===

'''Clicking''' on a one-letter code highlights the residue in the 3D model (JSmol panel). If click is done while holding one of the '''modifier keys''' (Shift, Ctrl, Alt) the 3D view zooms in onto the residue, and makes it the center of rotation.

~~'''3D to sequence'''~~

~~Clicking on an atom in the 3D view highlights the residue it belongs to, in the sequence listing.~~

{| class="wikitable"

! rowspan="2" | Sequence to 3D:

| '''Hovering''' the pointer over a one-letter code displays, above the sequence, the full ID of the residue and, in the case of hetero groups, its description.

|-

| '''Clicking''' on a one-letter code highlights the residue in the 3D model (JSmol panel). If click is done while holding one of the '''modifier keys''' (Shift, Ctrl, Alt) the 3D view zooms in onto the residue, and makes it the center of rotation.

|-

! 3D to sequence:

| Clicking on an atom in the 3D view highlights the residue it belongs to, in the sequence listing.

|}

==== Search box ====

(This is displayed at the right of the sequence panel)

Entering a residue name (as one-letter code) highlights all locations of that residue, both in the sequence listing and in the 3D model.

Entering a '''residue name''' (as one-letter code) highlights all locations of that residue, both in the sequence listing and in the 3D model.

Entering a sequence fragment (e.g. AAMGT, for Ala-Ala-Met-Gly-Thr) will highlight the locations of any matches in the sequence listing and also in the 3D model. (This may fail if gaps or microheterogeneity are involved.)

Entering a '''sequence fragment''' (e.g. AAMGT, for Ala-Ala-Met-Gly-Thr) will highlight the locations of any matches in the sequence listing and also in the 3D model. (This may fail if gaps or microheterogeneity are involved.)

Entering a number will highlight the residue with that number in both the sequence and the 3D model.

Entering a '''number''' will highlight the residue with that number in both the sequence and the 3D model.

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@@ Line 7: / Line 7: @@
 The purpose of this tool is to make it easy to relate sequence to 3D structure within any Proteopedia page. By design the listing is kept simple. Sequence annotations such as secondary structure or sequence motifs can be viewed in other databases, and need not be shown here.
-=== Description ===
+=== Description of sequence display ===
 Whenever a model is loaded into JSmol, a sequence listing is displayed for each chain. Chain is picked from a drop-down menu. If the model has a single chain, it will be displayed by default.
@@ Line 14: / Line 14: @@
 Both ribonucleotides and deoxyribonucleotides in nucleic acids are converted to single-letter.
-'''Sequence to 3D'''
+The sequence includes a combination of:
+* Residues with atoms that have coordinates (ATOM records in the file) and are also included in SEQRES records; these are displayed as uppercase letters.
+* Residues that lack coordinates but are mentioned in SEQRES records in the file (i.e. a physical gap, typically due to crystallographic disorder); these are displayed as lowercase letters; the reported residue number is an estimation, correlative to the adjacent residue with coordinates (an interpolated number is desirable but not currently implemented).
+* Residues inferred due to a numbering gap (absent from both SEQRES and ATOM records) are displayed as the number of missing residues surrounded by tilde (~) signs.
+* Residues in ATOM records that are absent in SEQRES records reflect sequence microheterogeneity; the alternate residues at the same sequence position are enclosed in square brackets.
+* Inserted residues are listed in-line with other residues, but displayed as superscript letters.
-'''Hovering''' the pointer over a one-letter code displays, above the sequence, the full ID of the residue and, in the case of hetero groups, its description.
+=== Interaction ===
-'''Clicking''' on a one-letter code highlights the residue in the 3D model (JSmol panel). If click is done while holding one of the '''modifier keys''' (Shift, Ctrl, Alt) the 3D view zooms in onto the residue, and makes it the center of rotation.
-'''3D to sequence'''
-Clicking on an atom in the 3D view highlights the residue it belongs to, in the sequence listing.
+{| class="wikitable"
+! rowspan="2" | Sequence to 3D:
+| '''Hovering''' the pointer over a one-letter code displays, above the sequence, the full ID of the residue and, in the case of hetero groups, its description.
+|-
+| '''Clicking''' on a one-letter code highlights the residue in the 3D model (JSmol panel). If click is done while holding one of the '''modifier keys''' (Shift, Ctrl, Alt) the 3D view zooms in onto the residue, and makes it the center of rotation.
+|-
+! 3D to sequence:
+| Clicking on an atom in the 3D view highlights the residue it belongs to, in the sequence listing.
+|}
 ==== Search box ====
 (This is displayed at the right of the sequence panel)
-Entering a residue name (as one-letter code) highlights all locations of that residue, both in the sequence listing and in the 3D model.
+Entering a '''residue name''' (as one-letter code) highlights all locations of that residue, both in the sequence listing and in the 3D model.
-Entering a sequence fragment (e.g. AAMGT, for Ala-Ala-Met-Gly-Thr) will highlight the locations of any matches in the sequence listing and also in the 3D model. (This may fail if gaps or microheterogeneity are involved.)
+Entering a '''sequence fragment''' (e.g. AAMGT, for Ala-Ala-Met-Gly-Thr) will highlight the locations of any matches in the sequence listing and also in the 3D model. (This may fail if gaps or microheterogeneity are involved.)
-Entering a number will highlight the residue with that number in both the sequence and the 3D model.
+Entering a '''number''' will highlight the residue with that number in both the sequence and the 3D model.