xmipp3.protocols.protocol_convert_pdb module
- class xmipp3.protocols.protocol_convert_pdb.XmippProtConvertPdb(**args)[source]
Bases:
ProtInitialVolumeConverts atomic structure files in PDB (Protein Data Bank) format into volumetric maps. Converting a PDB to a volume generates a simulated electron density map, useful for validating atomic models, fitting into experimental maps or performing docking.
Overview
The Convert PDBs to Volumes protocol transforms one or more atomic structure files (typically PDB, optionally CIF) into 3D volumetric density maps. The output is a simulated electron density map sampled on a 3D grid, at a user-defined voxel size (Å/px). This is a standard step whenever you want to bring an atomic model into the same “map space” used by cryo-EM.
From a user perspective, this protocol is most commonly used to: - compare an atomic model to an experimental cryo-EM map (visual inspection, fitting, validation), - generate a reference density from a known structure (for docking or alignment), - prepare model-based volumes for workflows that require volumes as input (e.g., projections, template-based comparisons), - convert multiple models into volumes in a consistent way (e.g., alternative conformations, homologs, mutants).
It is a practical bridge between atomic coordinates and volumetric cryo-EM representations.
Inputs and General Workflow Input structure(s)
You can provide either: - a single atomic structure (AtomStruct), or - a set of atomic structures (SetOfAtomStructs).
If you provide a set, the protocol converts each structure independently and outputs a set of volumes.
Sampling rate (Å/px)
This parameter defines the voxel size of the simulated volume. It should be chosen to match the voxel size of the experimental map you plan to compare against.
Practical rule: - If you will fit the simulated volume into an experimental map, use the same sampling rate as the experimental map. - If you only want a qualitative visualization, a slightly coarser sampling may be acceptable, but keep in mind it changes the apparent sharpness.
Defining the Output Box: Size and Origin
A crucial practical aspect of PDB→volume conversion is deciding the box size and (optionally) the origin of the output volume. This protocol offers two main strategies.
Option A — Use an existing volume as a template
“Use a volume as an empty template?” = Yes
You provide an input volume, and the protocol uses its: - box size - origin / coordinate frame
This is the best choice when your goal is direct comparison with an existing cryo-EM map, because it ensures that the simulated volume lives in the same grid and coordinate system.
Important practical note:
If you use a template volume, you should typically set Center PDB = No (advanced option). Otherwise, the protocol will re-center the model, which may break the intended correspondence with the template map.
Use this mode when: - you already have an experimental map and want the model density to match its frame exactly, - you are preparing volumes for subsequent alignment or difference-map analysis.
Option B — Define the output size explicitly
If you do not use a template volume, you can control the output size.
For a set of structures, you provide a single Box side size (px) that will be applied to all.
For a single structure, you may: - let the protocol estimate a reasonable size automatically, or - enable Set final size? and specify X (and optionally Y, Z).
Use this mode when: - you want standardized boxes across many models, - you are building references for downstream workflows that require fixed dimensions, - there is no existing experimental map that defines the coordinate frame.
Centering the Model Center PDB (advanced)
If enabled, the protocol centers the atomic model using its center of mass before generating the volume.
This is often convenient when: - you are generating a model map mainly for visualization, - you want the density centered in the box for general use, - you are converting multiple models and want consistent centering.
However, centering can be problematic if you are trying to preserve an external coordinate frame (for example when matching an experimental map or a template). In those cases, centering should usually be disabled.
Store centered PDB (advanced)
If you enable this option, the protocol will also save the centered PDB file(s) in the output directory. This is useful when you want to: - keep a record of the exact coordinates used, - reuse the centered structure in later docking or fitting steps, - share the centered model with collaborators.
CIF to PDB Conversion Convert CIF to PDB (advanced)
Some structures are distributed as mmCIF rather than PDB. If you enable this option, CIF inputs will be converted to PDB before volume generation.
This is generally safe for typical structures, but very large models can sometimes cause conversion difficulties. If conversion fails, a practical workaround is to: - disable conversion and use the CIF directly when possible in your workflow, or - convert the CIF externally using specialized tools before running the protocol.
Outputs and Their Interpretation
Depending on whether the input is a single structure or a set, you will obtain: - Output volume (single input). A single Volume object (typically saved as MRC), with the sampling rate set to your chosen value.
If you used a template volume, the output will also preserve the template’s origin/frame, which is essential for direct overlays.
Output volumes (set input). A SetOfVolumes, one volume per input
structure, all created using the same sampling rate (and the same box size if you specified one).
Output PDB / Output AtomStructs (optional). If you enabled Store centered
PDB, the protocol outputs the centered structure(s) linked to the generated volume(s). This is helpful for reproducibility: it lets you know exactly what model coordinates correspond to the simulated density.
Practical Recommendations
For model-to-map comparison, start by matching the sampling rate to the experimental map.
If you want the simulated volume to overlay the experimental map without additional alignment, use the template volume mode and disable centering.
If you are preparing generic references or a library of model maps, centering is often convenient and makes volumes easier to handle downstream.
If you plan to process many structures, use a SetOfAtomStructs input and define a consistent box size so all outputs are directly comparable.
After conversion, always visually inspect the output volume: - is the density fully inside the box? - is it centered as expected? - does the apparent size match the model?
Final Perspective
Converting atomic models to volumes is not just a file format transformation—it is a way to place atomic information into the same representation used by cryo-EM maps. The key practical choices are sampling rate, box definition, and whether to preserve an external coordinate frame.
Used carefully, this protocol provides reliable simulated densities that support fitting, validation, and biologically meaningful comparison between models and experimental reconstructions.
- OUTPUT_NAME1 = 'outputVolume'
- OUTPUT_NAME2 = 'outputVolumes'
- OUTPUT_NAME3 = 'outputPdb'
- OUTPUT_NAME4 = 'outputAtomStructs'