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stge4code

shelx-mcp

by stge4code
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Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault
SHELX_DIRECTORYYesPath to the folder containing SHELX executables (e.g., shelxl, shelxs, shelxt, etc.)

Instructions

Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.

This server publishes no instructions, or was last inspected before Glama recorded them.

Capabilities

Features and capabilities supported by this server

Protocol revision2025-11-25

CapabilityDetails
tools
{
  "listChanged": false
}
prompts
{
  "listChanged": false
}
resources
{
  "subscribe": false,
  "listChanged": false
}
experimental
{}

Tools

Functions exposed to the LLM to take actions

NameDescription
run_shelxA

Run a SHELX console program on supplied input files and return its output.

Args: program: one of shelxs, shelxl, shelxt, shelxc, shelxd, shelxe, ciftab. ins: full text of the .ins instruction file. hkl: optional text of the .hkl reflection file (needed for refinement). basename: base file name (no extension) used for inputs/outputs. workdir: directory to run in; a throw-away temp dir is used when omitted. timeout: seconds before the run is aborted. return_output: include the produced .res/.lst/.cif content in the reply.

Returns the program output, return code, and (if requested) the generated files.

solveA

Run structure solution (default SHELXS direct methods; use shelxt for dual-space).

Requires an .ins file set up for solution (TITL, CELL, ZERR, LATT, SYMM, SFAC, UNIT, plus a solution-specific instruction such as TREF or FMAP, and HKLF/END) and the corresponding .hkl data.

refineA

Run least-squares structure refinement with SHELXL (or CGLS via shelxt).

Requires a complete .ins file (with L.S. / CGLS and HKLF instructions) and the .hkl reflection data. Returns the .lst summary and refined .res model.

list_commandsA

List every SHELXL instruction the server knows about (alphabetical).

command_helpA

Return the SHELXL instruction signature and full description for name.

Example: command_help("ANIS") or command_help("L.S.").

search_commandsA

Search SHELXL instructions by keyword across names and descriptions.

list_solution_keywordsA

List the keywords (.ins cards, command-line options, or stdin keywords) for a SHELX solution program.

Unlike list_commands (which covers SHELXL refinement), this covers the programs that find or phase a structure: shelxs (direct methods), shelxd (dual-space small molecules), shelxd_mm (macromolecular substructure solution), shelxt (intrinsic phasing command-line switches), shelxc (SAD/MAD data-preparation stdin keywords) and shelxe (phasing command-line options).

Args: program: one of shelxs, shelxd, shelxd_mm, shelxt, shelxc, shelxe.

Returns the sorted keyword list, or a message if the program is unsupported.

solution_helpA

Return the signature and description for one SHELX solution keyword.

Covers shelxs / shelxd / shelxd_mm .ins cards (e.g. TREF, FIND, SHEL, DSUL), shelxt command-line switches (e.g. -a, -d, -L), shelxc stdin keywords (e.g. SAD, CELL, SPAG) and shelxe command-line options (e.g. -aN). Use list_solution_keywords first to discover valid names.

Args: program: one of shelxs, shelxd, shelxd_mm, shelxt, shelxc, shelxe. keyword: the instruction card, switch or option name (e.g. TREF, -a, SAD).

Returns the signature and full description, or a not-found message.

validate_insB

Check an .ins file for the SHELXL header cards required before HKLF/END.

Reports which mandatory cards (TITL, CELL, ZERR, LATT, SYMM, SFAC, UNIT, HKLF, END) are present, plus a few common mistakes.

analyze_resultsB

Summarise refinement metrics from SHELXL .lst and/or .res text.

Returns R1, wR2, GooF (S), max shift/esd, atom count and any warning lines.

analyze_solutionA

Summarise a SHELXT structure-solution run from .lxt and/or .res text.

SHELXT writes its console summary to name.lxt and its solution(s) to name_a.res, name_b.res, ... Pass the listing text as lxt and a solution model as res. Returns the R1, alpha (phase error), assigned space group, Flack x parameter and atom count of the reported solution.

shelx_infoA

Report which SHELX directory is configured and which programs are available.

Prompts

Interactive templates invoked by user choice

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription

No resources

Deploy Server
One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

TDQS

A3.8/5.0

Scored across 12 tools

Disambiguation4/5

Most tools have distinct purposes: run_shelx is a generic runner, while solve and refine are specialized wrappers that could be confused with it but are clearly described. The pairs list_commands/list_solution_keywords and command_help/solution_help are differentiated by domain (refinement vs. solution), but agents might initially pick the wrong one.

Naming Consistency4/5

Tool names are predominantly snake_case and verb-first (search_commands, validate_ins, analyze_results), but a few are noun-first (command_help, solution_help, shelx_info). The pattern is mostly consistent and readable, with minor deviations.

Tool Count5/5

With 12 tools, the server is well-scoped for the SHELX crystallography domain. Each tool covers a distinct aspect (running programs, getting help, validating input, analyzing output), and the count is within the ideal 3-15 range without feeling excessive.

Completeness5/5

The tool surface covers the full workflow: searching/listing/help for commands and keywords, running any SHELX program, dedicated solve/refine wrappers, input validation, output analysis, and environment reporting. No obvious gaps that would block a typical crystallographic workflow.

Maintenance

ActivityStale
ResponsivenessNo issues

Resources