Using GMOL
Using GMOL
This is a list of the functions added to GMOL for genome structure visualization. Accompanying each function listed is a short description of what it does as well as the syntax used to call it in the GMOL console. For examples of using these functions with the sample data provided, see the GMOL walkthrough.
Opening Files
To open a file in GMOL select "File -> Open" and browse for the desired file. Alternatively, simply click on the green folder icon and then browse for the desired file. IMPORTANT: File paths cannot contain spaces!
Basic Functionality
*NOTE: This section covers functions specific to GMOL. For information about additional functionality see the Jmol user guide at http://jmol.sourceforge.net/docs/JmolUserGuide/ *
scaledown
- Scales the structure down to the next lower level (more detailed).
- Type "scaledown" (without quotes) in the console or click the down blue arrow icon.
scaleup
- Scales the structure up to the next higher level (less detailed).
- Type "scaleup" (without quotes) in the console or click the up blue arrow icon.
select
- Selects units in the current structure based on index information.
- Type “select i” in the console to select a single unit where ‘i’ is the index of the unit, or “select i-j” to select a range of units where ‘i’ is the starting index and ‘j’ is the ending index. You can also click the red square with white arrow icon and then click on a unit in the structure to select a single unit or click and drag over the structure to select multiple units.
gselect
- Selects units in the current structure based on scale information.
- Type “gselect a,b,c,d” where ‘a’ is index of chromosome scale, ‘b’ is index of loci scale, ‘c’ is index of fiber scale, and ‘d’ is index of nucleosome scale. Setting any of the variables to 0 means that it is unspecified and all indices on that scale will qualify.
sselect
- Selects units in the current structure based on genome sequence information.
- Type “sselect X,a,b” where ‘X’ is the chromosome index number, ‘a’ is the starting position on the genome sequence, and ‘b’ is the ending position on the genome sequence.
Get Genome Sequence
- Outputs the genome sequence of the selected unit to the console
- After selecting a unit in the structure select “Tools -> Genome Sequence -> Choose Function -> Local Database Sequence Search/ Ensembl Sequence Search/ UCSC Genome Browser Sequence Search” and enter the desired starting and ending locations.
Get Basic Local Alignment Search Tool
- Outputs the BLAST result of genome sequence of the selected unit to a file saved locally
- After selecting a unit in the structure select “Tools -> Genome Sequence -> Choose Function -> NCBI BLAST” and enter the desired starting and ending locations.
Get Transcribe and Properties of Sequence
- Outputs the transcribe and properties result of genome sequence of the selected unit to the console
- After selecting a unit in the structure select “Tools -> Genome Sequence -> Choose Function -> Sequence Transcribe/ Sequence Properties” and enter the desired starting and ending locations.
Get Gene of Sequence
- Outputs the gene information result of sequence of the selected unit to the console
- After selecting a unit in the structure select “Tools -> Genome Sequence -> Choose Function -> Exons Introns” and enter the desired starting and ending locations.
More Help
For more information and assistance about GMOL and its features, check out the walkthrough.
Obtaining 3D genome Models
GMOL is used to visualize 3D genome models. There are a number of great tools used to generate these models for GMOL to visualize. Here are a few:
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