Fetch by ID EMDB + fit PDBs enhancement suggestion
Dear Chimera, Attempting to Fetch by ID an EMDB entry with a fitted model, where the model does exist in PDB format, causes an error: No such ID. The map is retrieved but not opened in Chimera. The two main reasons that the model is not available: A. The model is only available in mmCIF format. Since a wwPDB remediation at the end of last year, entries that are larger than what the PDB format can handle are no longer distributed as split entries. They are only distributed as mmCIF (and PDBx) files. This is common for say ribosomes. EMD-6315 with fitted model 3j9z is an example. Changing the command so that it attempts to retrieve mmCIF files rather than PDB files would fix this issue. B. The model has not been released, EMDB and PDB releases for maps and models are not always synchronised. An example would be EMD-6413, where the model 3jb9 is currently waiting for author approval. In this case it would be nice if the map was loaded. Many Thanks, Ingvar
Hi Ingvar, I’ve made Chimera fetch the mmCIF file if the PDB format file is not available. This will be in tonight’s daily build. Unfortunately the Chimera mmCIF file reader is very slow since it is written all in Python — opening 3j9z.cif, 150,000 atoms, took 40 seconds. I also fixed fetch EMDB + fit PDBs to show the map even if one or more PDBs are not found. Thanks for reporting these bugs. Tom
On Sep 18, 2015, at 5:10 AM, Ingvar Lagerstedt wrote:
Dear Chimera,
Attempting to Fetch by ID an EMDB entry with a fitted model, where the model does exist in PDB format, causes an error: No such ID. The map is retrieved but not opened in Chimera.
The two main reasons that the model is not available: A. The model is only available in mmCIF format. Since a wwPDB remediation at the end of last year, entries that are larger than what the PDB format can handle are no longer distributed as split entries. They are only distributed as mmCIF (and PDBx) files. This is common for say ribosomes. EMD-6315 with fitted model 3j9z is an example. Changing the command so that it attempts to retrieve mmCIF files rather than PDB files would fix this issue.
B. The model has not been released, EMDB and PDB releases for maps and models are not always synchronised. An example would be EMD-6413, where the model 3jb9 is currently waiting for author approval. In this case it would be nice if the map was loaded.
Many Thanks, Ingvar
Hi Tom, Thank you for the usual quick fixes. The daily build on the download page still says Sep/16, I will try out these changes when they become available. Ingvar On 18 Sep 2015, at 18:55, Tom Goddard <goddard@sonic.net> wrote:
Hi Ingvar,
I’ve made Chimera fetch the mmCIF file if the PDB format file is not available. This will be in tonight’s daily build. Unfortunately the Chimera mmCIF file reader is very slow since it is written all in Python — opening 3j9z.cif, 150,000 atoms, took 40 seconds. I also fixed fetch EMDB + fit PDBs to show the map even if one or more PDBs are not found. Thanks for reporting these bugs.
Tom
On Sep 18, 2015, at 5:10 AM, Ingvar Lagerstedt wrote:
Dear Chimera,
Attempting to Fetch by ID an EMDB entry with a fitted model, where the model does exist in PDB format, causes an error: No such ID. The map is retrieved but not opened in Chimera.
The two main reasons that the model is not available: A. The model is only available in mmCIF format. Since a wwPDB remediation at the end of last year, entries that are larger than what the PDB format can handle are no longer distributed as split entries. They are only distributed as mmCIF (and PDBx) files. This is common for say ribosomes. EMD-6315 with fitted model 3j9z is an example. Changing the command so that it attempts to retrieve mmCIF files rather than PDB files would fix this issue.
B. The model has not been released, EMDB and PDB releases for maps and models are not always synchronised. An example would be EMD-6413, where the model 3jb9 is currently waiting for author approval. In this case it would be nice if the map was loaded.
Many Thanks, Ingvar
Hi Ingvar, The Chimera 1 nightly builds were hung. We fixed it just now and tonight it should build the new code that fetches mmCIF files if the PDB format file does not exist. We do almost all of our development of Chimera 2 now (not yet released), so we sometimes don’t notice immediately when something goes awry with Chimera 1. Tom
On Sep 21, 2015, at 2:50 AM, Ingvar Lagerstedt wrote:
Hi Tom,
Thank you for the usual quick fixes. The daily build on the download page still says Sep/16, I will try out these changes when they become available.
Ingvar
On 18 Sep 2015, at 18:55, Tom Goddard <goddard@sonic.net> wrote:
Hi Ingvar,
I’ve made Chimera fetch the mmCIF file if the PDB format file is not available. This will be in tonight’s daily build. Unfortunately the Chimera mmCIF file reader is very slow since it is written all in Python — opening 3j9z.cif, 150,000 atoms, took 40 seconds. I also fixed fetch EMDB + fit PDBs to show the map even if one or more PDBs are not found. Thanks for reporting these bugs.
Tom
On Sep 18, 2015, at 5:10 AM, Ingvar Lagerstedt wrote:
Dear Chimera,
Attempting to Fetch by ID an EMDB entry with a fitted model, where the model does exist in PDB format, causes an error: No such ID. The map is retrieved but not opened in Chimera.
The two main reasons that the model is not available: A. The model is only available in mmCIF format. Since a wwPDB remediation at the end of last year, entries that are larger than what the PDB format can handle are no longer distributed as split entries. They are only distributed as mmCIF (and PDBx) files. This is common for say ribosomes. EMD-6315 with fitted model 3j9z is an example. Changing the command so that it attempts to retrieve mmCIF files rather than PDB files would fix this issue.
B. The model has not been released, EMDB and PDB releases for maps and models are not always synchronised. An example would be EMD-6413, where the model 3jb9 is currently waiting for author approval. In this case it would be nice if the map was loaded.
Many Thanks, Ingvar
participants (2)
-
Ingvar Lagerstedt -
Tom Goddard