---
title: "Molecular Replacement MOLREP"
url: "https://help.dectris.cloud/en/article/molecular-replacement-molrep"
language: "en"
last_updated: "2026-07-16T01:04:46.123Z"
---

# Molecular Replacement MOLREP

Run CCP4 MOLREP on DECTRIS D.LAB using an input MTZ and a reference model fetched from the PDB by code. The template downloads the PDB file, runs molrep with your chosen structure-factor labels, and copies all results into the job output directory.

## Introduction

[MOLREP](https://www.ccp4.ac.uk/html/molrep.html) is a program from the [CCP4](https://www.ccp4.ac.uk/) suite for performing **molecular replacement** in macromolecular crystallography. Given an experimental dataset and a suitable reference model, it determines the orientation and position of the model in the unit cell.

[This job template](https://app.dectris.cloud/sections/analysis/jobs/templates/public?id=019ad7f5-af13-7531-ab70-12f99e54aef0) illustrates how MOLREP can be run as a job on **DECTRIS D.LAB** using a configurable command-line workflow. The template is built on the **CCP4 & XDS & PyMOL command line** [**environment**](https://help.dectris.cloud/en/article/environments) and is executed in a non-interactive batch setting.

You provide an input MTZ file containing structure-factor amplitudes and a PDB code identifying a reference model. The template then:

-   prepares the CCP4 runtime environment,
-   downloads the reference structure from the Protein Data Bank (PDB),
-   runs MOLREP with configurable structure-factor labels and optional parameters such as the number of monomers, solvent fraction, and sequence information,
-   collects the resulting models, logs, and intermediate files into the job output directory.

The result is a reproducible molecular replacement workflow that can be reused across datasets by adjusting only the job input parameters.

## Quick Start

To run this job, valid input for the following variables is required:

-   **DC\_MTZ\_IN:** Path to an MTZ file containing structure-factor amplitudes and uncertainties.  
    Example: `/dectris_data/<project>/<experiment>/processed/processed_dir/merged.mtz`
-   **DC\_PDB\_CODE:** Four-character PDB identifier of the reference model to be used for molecular replacement.  
    Example: `1ABC`
-   **DC\_F\_LABEL:** Column label for structure-factor amplitudes (*F*) in the MTZ file.  
    Default: `F`
-   **DC\_SIG\_LABEL:** Column label for uncertainties (*SIGF*) in the MTZ file.  
    Default: `SIGF`
-   **DC\_N\_MONOMERS:** Expected number of monomers in the asymmetric unit.  
    Default: `0`
-   **DC\_SOLVENT\_FRACTION:** Solvent fraction of the crystal (e.g. `0.45`).  
    Default: `0`
-   **DC\_SEQ\_FILE:** Path to a sequence file (FASTA format).  
    Default: `/path/to/seq.fasta$`

![](https://cdn-assets.productfruits.com/a4d21016-f196-41bb-a28b-e7bd02afcc53)

## Output

![](https://cdn-assets.productfruits.com/2f2930e1-2e58-4928-aaf8-3e36c0321662)

A successfully completed job produces the following output files in the job output directory:

-   **1ABC.pdb**: The reference model downloaded from the Protein Data Bank (PDB) using `DC_PDB_CODE`. This is the input search model provided to MOLREP.
-   **molrep.pdb:** The molecular replacement solution produced by MOLREP (placed and oriented model in the target unit cell).
-   **molrep.doc:** MOLREP log/documentation file containing run parameters, MTZ label interpretation, search progress (rotation/translation results), scores, and summary statistics.

## Versions

### **Version 1**

-   Adds `molrep.doc` to the job table output.  
    Built with **version 3** of the CCP4 & XDS & PyMOL command line environment.

### **Version 0**

-   Initial version of the MOLREP job template.  
    Built with **version 3** of the CCP4 & XDS & PyMOL command line environment.