Membrane Templates¶

OpenBuilder supports loading membrane compositions from CSV or OpenBuilder template (.ob) files. This feature allows users to quickly generate reproducible membrane systems and batch-create multiple membrane compositions from a single file.

Complete Example¶

# ExampleMembrane1

;resname,upper_leaflet,lower_leaflet,apl_upper,apl_lower
POPC,0.60,0.40,0.61,0.61
DOPC,0.25,0.40,0.67,0.67
CHOL,0.15,0.20,0.40,0.40

# ExampleMembrane2

;resname,upper_leaflet,lower_leaflet,apl_upper,apl_lower
POPC,0.60,0.20,0.61,0.61
DOPC,0.25,0.20,0.67,0.67
CHOL,0.15,0.60,0.40,0.40

This example defines two asymmetric membranes composed of POPC, DOPC, and cholesterol.

File Structure¶

A template consists of one or more membrane definitions.

Each membrane definition starts with a name line:

# MembraneName

The membrane name is used for:

Template identification
Replica folder naming
Output organization

If only a single membrane composition is required, the name line can be omitted and the file may be used as a standard CSV.

Template Format¶

Lines starting with ; are treated as comments and ignored by OpenBuilder. Each lipid is defined on a separate line:

; resname,upper_leaflet,lower_leaflet,apl_upper,apl_lower

Columns¶

Column	Description
`resname`	Lipid residue name
`upper_leaflet`	Ratio or count in the upper leaflet
`lower_leaflet`	Ratio or count in the lower leaflet
`apl_upper`	Area per lipid (nm²) in the upper leaflet
`apl_lower`	Area per lipid (nm²) in the lower leaflet

Single Membrane Example¶

;resname,upper_leaflet,lower_leaflet,apl_upper,apl_lower
POPC,0.70,0.30,0.61,0.61
DOPC,0.30,0.70,,

Missing APL values automatically receive the default value of 0.60 nm².

Multiple Membrane Definitions¶

A single file may contain multiple membrane compositions.

# PlasmaMembrane

;resname,upper_leaflet,lower_leaflet,apl_upper,apl_lower
POPC,0.70,0.30,0.61,0.61
DOPC,0.30,0.70,,

# CholesterolRich

;resname,upper_leaflet,lower_leaflet,apl_upper,apl_lower
POPC,0.50,0.40,0.61,0.61
CHOL,0.50,0.60,0.40,0.40

Each membrane will be processed independently.

Area Per Lipid APL¶

APL controls membrane packing density.

APL	Effect
Smaller values	Tighter packing
Larger values	Looser packing

If omitted:

POPC,0.70,0.30

or

POPC,0.70,0.30,,

OpenBuilder assigns 0.60 nm² automatically.

Ratios and Absolute Counts¶

Two composition modes are supported.

Relative Ratios¶

POPC,0.70,0.30
DOPC,0.30,0.70

Absolute Counts¶

POPC,70,30
DOPC,30,70

Warning

Do not mix ratios and absolute counts within the same membrane definition.

Supported File Types¶

OpenBuilder accepts:

.csv
.ob

Both formats use the same internal structure.