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– Import coordinates from a PDB file into a CCPN project
– Import coordinates from a CCPN project into a PDB file
– Import restraint files from a CCPN project to a PDB file
– Import restraints from a PDB file to a CCPN project
– Import shift files from a CCPN project to a PDB file
– Import shifts from a PDB file to a CCPN project
– Import shift files from a CCPN project to a PDB file
– Import FFT files of logs from a CCPN project to a PDB file

– All computations are done on the fly
– Very easy access to the program allowing for a quick and easy set up of the data
– User profile to allow user-specific settings
– Multi-threaded to perform heavy duty tasks
– A graphical user interface to help the user in getting started easily
– A restricted but flexible data access, without key authorization
– An option to write back the results and log files
– User-specific settings
– Several command line options
– Supports cases where you have to convert structures from PDB to CCPN format (CCPN lab format)
– Several services are exposed over the web to allow external access (e.g. If you are a user of RCSB PDB), or you want to use the program locally.
– Export coordinate files in the CCPN archive format
– Export coordinate files with the PDB format

What’s new in this version

2014-11-15: This version contains several bug fixes and a major refactoring.
– Support for networks in restraints
– Choice of the DUMP keyword
– Preview of the FFT log file
– Best fit for PDB files
– New: interactive help
– New: option to disable key authorization
– Option to skip errors in logs (empty messages)
– Import from CIF files
– User profile can now be saved for later use
– You are able to start a new project from an existing project

Changes in version

2014-10-22: This version contains a major refactoring and a few bug fixes.
– Improved performance
– Improved error handling
– Improved logging to the screen
– Import of 3D coordinates
– Improved support for blank entries in the PDB format
– New: options to provide a filename to write the results to (experimental

PDBeImporter [Mac/Win]

PDBeImporter provides a tool to import coordinates, shift-sets and restraints into the CCPN project format. It allows the following operations:

Importing structure coordinates: There are two ways of doing this:

From a PDB file

Using the editor, you can make a selection from a PDB file in the Structure Viewer, click the Import button, select a folder where the structure is and click Next.
If you wish, you can move the selected PDB file to a new location with the Move button (the PDB file will be replaced).

From a coordinate file

You can also import coordinates directly, using the Coordinate File Export function (see Export below).

Using Shift-Sets

A Shift-Set is a set of restraints defining the orientation and torsion angles of different chemical groups in your molecule, such as α or β-phosphoryl groups, amide groups, guanidinium groups etc.

Using Constraints

Constraints define whether or not a bond should be present or should be absent. The first constraint in a Set represents the absence of the bond, the last one represents its presence.

Please note that all atoms belonging to chemically related groups must be in the same Shift-Set. For example, all phosphoryl groups (such as the α-P of aspartate and the β-P of arginine) should have the same shift value (value = 5).

Example :

In the following example, we want to establish a Shift-Set of β-phosphoryl groups. First, we note the Shift-Set tab, which is selected by default.

Then we click the Add button, a new Shift-Set is created in the context of the current molecule, and we can begin entering the parameters: the name (α), the Shift (value = 5) and the Constraint (present).

Then, for each phosphate group, we type “β” (this shortcut will automatically generate the constraint “β” = 5), the name of the atom (P) and the chemical group to which it belongs (N or O).

If we want to apply this Shift-Set to all phosphoryl groups, we click the Apply button at the bottom of the Shift-Set panel.

All the new groups that were not present in the original structure will be treated in the same manner.


1) It allows you to import coordinates or restraints into a CCPN project as you can in the classic Web interface, either from a ccpNMR or ccpNMR XML file.
2) It allows you to define a project, a file of scripts, and a list of projects to import. It executes scripts for you when you request the import of a project file. So you do not have to have access to a shell in an XSEDE machine.
3) It provides an easy way to generate all the files necessary to communicate with the structure repository in the case of a structure deposition.
4) It provides an easy way to check files or project files before you upload them to the repository, so as to be ready for a structure deposition.
5) It provides an easy way to request a structure deposition.
6) It provides a way to link information from the repository to structure depositions.
7) It provides a way to export complex information:
— A web link for each change of coordinates
— A summary of the insertion at the bottom of the page of the current project
— A summary of the metadata at the bottom of the page of the current project
— A way to access directly to the metadata of the structure deposition
8) It provides a way to automate the action of requesting a deposition from the repository. This action may be done automatically when a structure deposition is requested.
9) It provides a way to view a “screen” during the preparation of a structure deposition.
10) It provides a centralized way to view the dependencies of a project file.
11) It provides a way to upload structure depositions in directories.
12) It provides a way to check the project file syntax.
13) It provides a way to validate a project file.
14) It can communicate directly with the XSEDE NMR.
This is PDBeImporter Documentation.
1) Get the wheel for the version of Python you are using.
Python 2.7:
From the official Python website :
Python 3.2:
From the official Python website :
Python 2.7:
From the PIP package manager:
curl -O

What’s New In PDBeImporter?

Imports a given coordinate set as ccp4 format into a CCPN project.
You can also import restraints in ccp4, as well as any constraints in the format (I.J, K.L, Z(D)) for an unique or X.Y, K.L, Z(D) and Z(D).
There is no dependencies to PDBe.
It should also allow to import the information coming from other databases: such as JCSG-DB, CARD, HSEARCH, BMRB…

“PDBeImporter” tool

See PDBeImporter Tutorial for additional information.


To install this PyPI package (The “pip” tool of Python), just run the following command in your terminal :

pip install PDBeImporter

The basic usage :

# Import the coordinates of the NMR structure of the inhibitor HCV-D3 into a CCPNproject.
# The idea is to grab the ccp4 format which can be created by a command such as :
#./ccp4_convert -d -c
#%pdbe_importer_from_ccp4 hcvd3_.coordinates
#%pdbe_importer_from_ccp4 hcvd3_.shifts

Tips and notes

To use this tool :
– the coordinates must have been exported by “ccp4_convert”
– the coordinates and the constraints of the NMR structure must be in ccp4 format
– you can import constraints (such as JCSG-DB, CARD or HSEARCH)

If you want to use the coordinates coming from PDBe, you may run :
%pdbe_importer_from_ccp4 -h

and the usage of this tool is :
%pdbe_importer_from_ccp4 hcvd3_.coordinates
%pdbe_importer_from_ccp4 hcvd3_.shifts
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