[3dem] Twelve golden rules for deposition of EM data in EMDB and PDB

outreach at emdatabank.org outreach at emdatabank.org
Fri Jul 20 09:41:32 PDT 2012


Dear 3DEM List Members,

 

Every now and then depositors of EM data approach us with questions (or
gripes) about the deposition process, in particular when both a map and a
model are to be deposited. We appreciate that the process at present is not
ideal, since there are two separate deposition systems to deal with (EMdep
for EM maps and AutoDep or Adit for atomic coordinate models). The wwPDB and
EMDataBank partners are currently developing a new joint Deposition and
Annotation system that will be used by all deposition sites and with which
you will be able to deposit maps and models at the same time. We expect this
new system to go live next year. To make deposition a little bit easier in
the meantime, we have formulated a few “golden rules.”

 

Here is what you need to do to deposit EM volume data (incl. tomographic
reconstructions):

 

1.            Deposit the final reconstruction(s) in EMDB.

 

We do not archive raw data or intermediate steps of your structure
determination and it is only the final reconstructions and some information
describing the experiment that need to be uploaded or entered via the EMdep
deposition system (UK site: pdbe.org/emdep, US site: emdep.rutgers.edu).

 

 

2.            Your map must be in MRC, CCP4 or Spider format; it may
optionally be compressed.

 

To upload a compressed map, use zip, gzip or bzip2 compression schemes. All
uploaded maps will be converted by us and archived and distributed as CCP4
files (ftp://ftp.wwpdb.org/pub/emdb/doc/map_format/EMDB_mapFormat_v1.0.pdf
). Files uploaded in MRC format need to follow a strict interpretation of
the file-format description (http://www2.mrc-lmb.cam.ac.uk/image2000.html ).
Note that many programs generate “.mrc” files that are modifications or
extensions of the MRC format. In the best-case scenario, the deposition
system will ignore the additional information, but some modifications may
lead to errors during the reading of the map-header parameters, and in the
worst case they will crash the deposition system.

 

 

3.            Please check the converted map.

 

Once your map has been converted into CCP4 format, EMdep will now allow you
to download the converted map. Please do this and check the map visually,
check the density range, and check that the map overlaps with any fitted
models you are planning to deposit in the PDB.

 

 

4.            You can deposit only one map per session.

 

The deposition session assigns one accession code (EMD-nnnn) to one map.
Therefore, even if your experiment resulted in multiple maps (e.g.,
heterogeneous data separated into multiple reconstructions), each one has to
be deposited in a separate session. To make deposition easier, use the
option “Based on previous submission” in EMdep - this will populate many of
the fields in the deposition form based on the previous submission.

 

 

5.            The voxel spacing used in the map must be specified.

 

The voxel spacing (Ångstroms per pixel in X, Y, and Z) is crucial for
determining the physical dimensions of the map. The numbers entered in EMdep
will be used to rescale the map!

 

 

6.            The contour level of the map must be specified, except for
tomographic reconstructions.

 

The contour level is important for the interpretation of the map. It defines
the surface of the structure, and calculation of volume and molecular mass
are dependent on it. 

 

 

Once you have uploaded a map, you have the option to deposit a “fitted
model” to the PDB. Such a model can be the result of a rigid-body docking of
an existing PDB entry, or it may be the result of docking plus refinement
(e.g., flexible fitting), or it may have been determined de novo using the
EM map alone. Please note that the two EMDB deposition sites use the same
software for EM depositions (EMdep), but different software for PDB
depositions - the European site (PDBe at EBI) uses AutoDep and the US site
(RCSB PDB) uses Adit. Here is what you need to do:

 

7.            Always deposit the EM map first (in EMDB) and then any fitted
models (in the PDB).

 

Always start by depositing the EM map as described above. Towards the end of
your deposition, you will get the option to deposit your fitted models to
the PDB. This option will remain active even after you have submitted your
EM map.

 

 

8.            Deposit your fitted models in the PDB.

 

All fitted models may be deposited, even if they are the result of
rigid-body transformation of an existing PDB model. If the map doesn’t
support atomistic interpretations because of lack of resolution, consider
omitting water molecules, small ligands, ions, and side chains, or providing
a C-alpha trace (for proteins) or a phosphorus trace (for polynucleotides).

 

 

9.            Model coordinates must be in the same reference frame as the
EMDB map.

 

Your model must fit the map that will be archived in EMDB, i.e., the result
of the conversion to CCP4 format by the deposition process. See golden rule
#3.

 

 

10.         For symmetric models the atomic coordinates should only include
the asymmetric unit.

 

When you deposit your model you can provide the transformation matrices that
are required to generate the complete assembly.

 

 

11.         The correct model sequence must be specified.

 

This can be confusing! In cases where the sequence of the fitted model
differs from that of the EM map, it is the former that needs to be specified
during the deposition of the fitted model. However, the genus/species
description entered in both the EMDB and PDB depositions should be that of
the sample on which the EM data was collected.

 

 

12.         Your model must make chemical and physical sense.

 

If the atomic coordinates represent a composite model (made of two or more
separate models) make sure they do not clash or overlap with each other.
Flexible fitting may introduce incorrect chirality into the model. All such
errors or problems should be corrected prior to deposition. There are
standard software packages available to carry out these kinds of geometric
checks (e.g., MolProbity (http://molprobity.biochem.duke.edu/) and WhatCheck
(http://swift.cmbi.ru.nl/gv/whatcheck/)).

 

 

You can find more information about EM deposition under “Additional Links”
on the EMDataBank deposition page (http://www.emdatabank.org/deposit.html).
For specific questions, please feel free to contact us at:
help at emdatabank.org

 

On behalf of EMDataBank – Ardan Patwardhan and Cathy Lawson

 

 

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