Seqtool: Difference between revisions

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Angel Herraez (talk | contribs)
Editor, Macro, Print3D, Tester
1,212 edits
documenting the SequenceTool
Angel Herraez (talk | contribs)
Editor, Macro, Print3D, Tester
1,212 edits
documenting the SequenceTool
Line 14: Line 14:
Both ribonucleotides and deoxyribonucleotides in nucleic acids are converted to single-letter, too.
Both ribonucleotides and deoxyribonucleotides in nucleic acids are converted to single-letter, too.


The sequence includes a combination of:
The sequence includes information combined from the COORD and SEQRES records in the pdb file:
* 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).
{| class="wikitable"
* 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.
| uppercase letters || Residues with atoms that have coordinates (ATOM records in the file) and are also included in SEQRES records
* 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.  
| 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.
|}


=== Interaction ===
=== Interaction ===
Retrieved from "https://proteopedia.org/Seqtool"