Mapiya - contact maps

Basic options

contact cutoff [Å]*

protonation pH*

Advanced options

Hydrogen bonds*

Secondary structure*

Electrostatics*

Fix structure

add atoms*

add residues*

↳ max loop length*

keep heterogens*

replace non-standard aa*

apply mutations

Add environment

add environment*

↳ positive ion*

↳ negative ion*

↳ ionic strength*

↳ water box*

• ↳ box dimensions*

↳ lipid type*

↳ membrane position*

Clicking the option below will invoke the reconstruction of the biological assembl(y/ies) using the information in the input PDB file ('REMARK 300 and 'REMARK 350').
More information is provided in the About section.

Create separate projects for each biological assembly

Reset to defaults

For more info see About page

or

Download structure from the rcsb.org

1. Select Options

This section allows you to select the basic parameters of the structure analysis to be performed. If you are not sure which options to select, leave them at their default settings. Note that invoking additional calculations may increase the calculation time.

2. Fix Structure

This section allows you to repair or modify the structure using PDBfixer. You can add missing atoms, residues, loops or convert non-standard residues to their standard equivalents.

3. Biological Assembly

This section enables reconstruction of the biological assembl(y/ies) using the information in the input file PDB ('REMARK 300 and 'REMARK 350'). More information is provided in the About section.

4. Upload file

Finally you can upload your files by dropping them into the dropbox, or you can download a structure from the Protein Data Bank. PDB file format is required.