Seqtool
From Proteopedia
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To have SeqTool in your page, add <code><b><seqtool/></b></code> in the wikitext, including the <b>/</b> after the word "seqtool". It is recommended to put that outside and before the <code><StructureSection></code> tag, so that the full width of screen is available for the sequence display and its search box. | To have SeqTool in your page, add <code><b><seqtool/></b></code> in the wikitext, including the <b>/</b> after the word "seqtool". It is recommended to put that outside and before the <code><StructureSection></code> tag, so that the full width of screen is available for the sequence display and its search box. | ||
| - | + | The purpose of this tool is to make it easy to relate sequence to 3D structure within any Proteopedia page. The listing is kept simple on purpose; sequence annotations such as secondary structure or sequence motifs can be viewed in other databases, and need not be shown here. | |
| - | + | ||
| - | The purpose of this tool is to make it easy to relate sequence to 3D structure within any Proteopedia page. | + | |
=== Description of sequence display === | === Description of sequence display === | ||
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Whenever a model is loaded into JSmol, a sequence listing is displayed for each chain. For saving space, only one chain is displayed at a time; such chain may be chosen from a drop-down menu. If the model has a single chain, it will be displayed by default. | Whenever a model is loaded into JSmol, a sequence listing is displayed for each chain. For saving space, only one chain is displayed at a time; such chain may be chosen from a drop-down menu. If the model has a single chain, it will be displayed by default. | ||
| - | The sequence is presented using the one-letter code for each amino acid residue. Ligands (hetero groups) and non-standard residues are displayed as "x" and positioned according to | + | The sequence is presented using the one-letter code for each amino acid or nucleotide residue. Ligands (hetero groups) and non-standard residues are displayed as "x" and positioned according to the residue/group number they have in the PDB file. Water and solvent groups are omitted by default. |
| - | + | ||
| - | The sequence includes information combined from the COORD and SEQRES records in the | + | The sequence includes information combined from both the COORD and SEQRES records in the PDB file: |
{| class="wikitable" | {| class="wikitable" | ||
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| [ ] || Alternate residues at the same sequence position (sequence microheterogeneity). These are present in ATOM records but absent in SEQRES records. | | [ ] || Alternate residues at the same sequence position (sequence microheterogeneity). These are present in ATOM records but absent in SEQRES records. | ||
|- | |- | ||
| - | | superscript letters || Inserted residues. | + | | superscript letters || Inserted residues (i.e., numbered with an insertion code in the file). |
|} | |} | ||
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{| class="wikitable" | {| class="wikitable" | ||
! rowspan="2" | Sequence to 3D: | ! rowspan="2" | Sequence to 3D: | ||
| - | | '''Hovering''' the pointer over a one-letter code | + | | '''Hovering''' the pointer over a one-letter code will display, above the sequence, the full ID of the residue and, in the case of hetero groups, its description. |
|- | |- | ||
| - | | '''Clicking''' on a one-letter code | + | | '''Clicking''' on a one-letter code will highlight 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 will zoom in onto the residue, and will make it the center of rotation. |
|- | |- | ||
! 3D to sequence: | ! 3D to sequence: | ||
| - | | Clicking on an atom in the 3D view | + | | Clicking on an atom in the 3D view will highlight the residue it belongs to, in the sequence listing. |
|} | |} | ||
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(This is displayed at the right of the sequence panel) | (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 (using top and bottom lines) and in the 3D model (using halos). |
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.) | ||
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| + | === Background information === | ||
| + | This implements most of the features included in a 2006 proposal by Eric Martz, described at [https://proteopedia.org/wiki/fgij/seqspecs.htm seqspecs.htm]. | ||
| + | |||
| + | <!-- | ||
=== Background info === | === Background info === | ||
| - | ''This is the specification, it should be incorporated in the help above.'' | + | ''This is the specification, it should be incorporated in the help above.'' DONE |
| - | Implementation of a 2006 proposal by Eric Martz, described at [ | + | Implementation of a 2006 proposal by Eric Martz, described at [http://firstglance.jmol.org/seqspecs.htm seqspecs.htm]. |
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C. Listing Examples | C. Listing Examples | ||
| - | Experience with Protein Explorer has shown that it is quite easy to find any sequence number by moving the mouse over the listing, and watching the number reports in the form slot. Here is the slot as it appears in Protein Explorer when residue 27, insertion code A, is touched in the sequence listing for the example below, 1QKZ chain L: | + | Experience with Protein Explorer has shown that it is quite easy to find any sequence number by moving the mouse over the listing, and watching the number reports in the form slot. Here is the slot as it appears in Protein Explorer when residue 27, insertion code A, is touched in the sequence listing for the example below, 1QKZ chain L: (done) |
| - | + | ||
This reporting slot will be immediately above the sequence listing. Thus, it is not important that the sequence number of a residue be apparent from inspection of the sequence listing table itself. Indeed, maintaining a correspondence between column and row and sequence number is not always feasible because of the anomalous sequence numberings used by some authors (see examples listed above). In the listing below, residues are divided into three groups of ten per line. However, the listing may start at a number <1 or >1, so line 1 need not be numbered 1-30. In the example below, it includes residues numbered 1-27C (1-27 plus 27A, 27B, 27C). | This reporting slot will be immediately above the sequence listing. Thus, it is not important that the sequence number of a residue be apparent from inspection of the sequence listing table itself. Indeed, maintaining a correspondence between column and row and sequence number is not always feasible because of the anomalous sequence numberings used by some authors (see examples listed above). In the listing below, residues are divided into three groups of ten per line. However, the listing may start at a number <1 or >1, so line 1 need not be numbered 1-30. In the example below, it includes residues numbered 1-27C (1-27 plus 27A, 27B, 27C). | ||
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L YSMSSTLTLTKD EYERHNSYTC EATHKTST | L YSMSSTLTLTKD EYERHNSYTC EATHKTST | ||
L SPIVKSFNRNE | L SPIVKSFNRNE | ||
| - | |||
| - | |||
<Insertions at | <Insertions at | ||
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Protein Explorer Seq3D Snapshots Illustrating Uses of Color | Protein Explorer Seq3D Snapshots Illustrating Uses of Color | ||
| + | |||
| + | --> | ||
Current revision
SeqTool displays the sequence of the structure in the JSmol applet.
To have SeqTool in your page, add <seqtool/> in the wikitext, including the / after the word "seqtool". It is recommended to put that outside and before the <StructureSection> tag, so that the full width of screen is available for the sequence display and its search box.
The purpose of this tool is to make it easy to relate sequence to 3D structure within any Proteopedia page. The listing is kept simple on purpose; sequence annotations such as secondary structure or sequence motifs can be viewed in other databases, and need not be shown here.
Contents |
Description of sequence display
Whenever a model is loaded into JSmol, a sequence listing is displayed for each chain. For saving space, only one chain is displayed at a time; such chain may be chosen from a drop-down menu. If the model has a single chain, it will be displayed by default.
The sequence is presented using the one-letter code for each amino acid or nucleotide residue. Ligands (hetero groups) and non-standard residues are displayed as "x" and positioned according to the residue/group number they have in the PDB file. Water and solvent groups are omitted by default.
The sequence includes information combined from both the COORD and SEQRES records in the PDB file:
| uppercase letters | Residues with atoms that have coordinates (ATOM records in the file) and are also included in SEQRES records |
| lowercase letters | Residues that lack coordinates but are mentioned in SEQRES records in the file (i.e. a physical gap, typically due to crystallographic disorder). The residue number reported is an estimation, correlative to the adjacent residue with coordinates (an interpolated number is desirable but not currently implemented). |
| ~number~ | Number of correlative residues inferred due to a numbering gap (absent from both SEQRES and ATOM records) |
| [ ] | Alternate residues at the same sequence position (sequence microheterogeneity). These are present in ATOM records but absent in SEQRES records. |
| superscript letters | Inserted residues (i.e., numbered with an insertion code in the file). |
Interaction
| Sequence to 3D: | Hovering the pointer over a one-letter code will display, above the sequence, the full ID of the residue and, in the case of hetero groups, its description. |
|---|---|
| Clicking on a one-letter code will highlight 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 will zoom in onto the residue, and will make it the center of rotation. | |
| 3D to sequence: | Clicking on an atom in the 3D view will highlight 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 (using top and bottom lines) and in the 3D model (using halos).
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.
Background information
This implements most of the features included in a 2006 proposal by Eric Martz, described at seqspecs.htm.
