Skip to main content
Glama

bfactor_view

Color protein structures by crystallographic B-factor to identify rigid cores, dynamic loops, and disordered regions. Blue-white-red cartoon.

Instructions

Colors the structure by crystallographic B-factor (temperature factor).

Blue = rigid/ordered (low B), white = intermediate, red = flexible/disordered (high B). Useful for identifying dynamic loops, disordered termini, and rigid structural cores. Shown as cartoon on black background.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
obj_nameYesPyMOL object name (e.g. "1abc")

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full burden of behavioral disclosure. It discloses the color scheme (blue/white/red), the display mode (cartoon), and background (black), which are the key behavioral traits. It does not mention potential side effects like overwriting existing colors, but the view-tool nature and description are sufficiently transparent.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is four sentences, each earning its place: it states the purpose, explains the color legend, gives use cases, and notes the display style. It is front-loaded and free of fluff.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a single-parameter visualization tool with an output schema present, the description is complete. It covers purpose, visual interpretation, applications, and rendering details, which is all the agent needs to decide on and invoke the tool correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the sole parameter obj_name is already well-documented in the schema. The description adds no additional information about the parameter, so it does not exceed the baseline of relying on the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states a specific verb ('Colors') and resource ('the structure by crystallographic B-factor'), immediately distinguishing it from sibling view tools like plddt_view or conservation_view. The naming and details about color mapping remove ambiguity about what the tool does.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides explicit use cases ('identifying dynamic loops, disordered termini, and rigid structural cores'), giving the agent context for when to invoke this tool. It does not explicitly mention when-not-to-use or name alternative tools, but the specificity of B-factor makes the intended scenario clear.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/chemrich/MCPymol'

If you have feedback or need assistance with the MCP directory API, please join our Discord server