Overview – Why Reciprocal Net?Why Reciprocal Net?

The motivating force behind the Reciprocal Net is to make life easier for the crystallographer as well as to insure that the colleague he is working with can make maximum use of the information obtained from a crystal structure analysis.

• Easy access to tabular information

• User friendly graphics

Current Status

Today we have nearly 20 systems either on-line or nearing on-line status, and the software is remarkably stable.

The system is not only popular with the users of the data, but has been widely recognized by several major scientific organizations:

• One of top 50 Science and Engineering sites (Scientific American)

• Featured on NetWatch in Science

• Featured in Chemistry (ACS general public newsletter)

Current Status

• Reciprocal Net Site Software 0.9.0 is currently scheduled for release in July, 2005

• If time and resources permit, a minor upgrade will be released in September, 2005; likely to be labeled 1.0.0

Portal and Educational Content

Portal and Educational Content

Portal and Educational Content

Portal and Educational Content

Portal and Educational Content

What is a LIMS?What does it look like?

Open a browser

What is a LIMS?• LIMS: Laboratory Information Management System

– Records data about laboratory operations and results– Supports workflow tracking, sample status reporting, and other

data-centric features (depending on the particular LIMS)

• The Reciprocal Net LIMS– Designed for crystallography– Workflow based– Maintains permanent, complete history– Stores selected miscellaneous data as well as files

What is a LIMS?

LIMS: Basic Workflow

• Many data reside in a database on the server

• Per-sample data include arbitrary files supplied by users

• ALL data are versioned

LIMS: Data Structure

When a new sample arrives in the facility, the procedure is:

– Submit the sample into the Reciprocal Net.– Collect some data and try to determine a unit cell.– Either “failed to collect” for examinations or “collect

preliminary data” and enter unit cell parameters, etc.– If the latter: collect full data, solve structure, early

refinement.– “Refine structure” and submit preliminary files.– Complete refinement, fill in the blanks in the data

mask, generate the graphics files and place as many files in the repository as you want.

LIMS: New Samples

When a structure has been published:

– Perform the “Release to Public” action

– Perform an “Add Citation” action if there is a citation

Release to Public

LIMS: How the IUMSC benefits• Sample tracking

– What is its current status

• No more paper reports

• Quick access to summary data about previously-determined structures– Search by unit cell parameters / volume– Search by sample provider / submitter– Search by (partial) sample number– Search by responsible crystallographer

Benefits

LIMS: More Benefits• Collaborating Chemists can do more for themselves

– Preparation of images– Tracking their samples’ status– Answering many structure geometry questions

• Ease of file exchange

• Files and data are accessible from anywhere with a network connection.

More Benefits

LIMS: More BenefitsThe Graphics Files

In order for the graphics to appear in the Reciprocal Net window, two files need to be in the repository: name.sdt and name.crt. The first contains a list of the atoms in ORTEP format, the second one a list of the atoms with cartesian coordinates, connectivity, and some other information.

The generation of these two files is a little weird.

Overview – Why Reciprocal Net?Generating files for graphics

If you have a straight-forward and “clean” molecule with Z’ = 1, and no disorders, the process is relatively simple: SHORTEP requires only a simple knowledge of some simple instructions and will proceed with not problems.

In many cases however, it is desirable to have a series of name.crt and name.sdt files to represent different moieties or ignore disordered portions of a molecule. It might also be desirable to have files in which only selected hydrogen atoms are shown.

XP allow to generate a name.ins file that contains precisely those atoms you want to see in the graphics application. The program shel2sdt.exe can read shelx .ins format and generate a file name.sdt, which can be read by SHORTEP.

Overview – Why Reciprocal Net?shortep.exe

SHORTEP is a legacy program that was developed in the IUMSC when there were few other options. The name comes from the fact that it is a “shortened” version of C. Johnson’s ORTEP program. All of the atom plotting instructions are removed, but the atom manipulation routines are retained, and a fair number of new manipulation and generation options are added.

Because we had standardized on a hybrid of GENLES (LANL) and ORFLS (ORNL) input formats, we were using (and still use) a unique “SDT” format. This is the nnnn.sdt file that is required for some of the graphics options in the Reciprocal Net.

The SHORTEP program can read an SDT and generate additional SDT’s as well as the nnnn.crt files used in recipnet.

The nnnn.crt file is the other file format that was employed, primarily to keep the file size minimized in the system.

Overview – Why Reciprocal Net?Generating files for graphics

nnnn.resfrom SHELX

shel2sdt.exe

nnnn.cif

shortep.exe

Manipulate atoms if necessary for differentfragments of interest.

nnnn.crt

nnnn.sdt

If one wishes to generate the files directly from a .res or .ins file

Overview – Why Reciprocal Net?shel2sdt

shel2sdt.exe is a command line program that can be used to create the name.sdt, which can be read into shortep.exe.

shel2sdt name.ins

is all you need to type.

SHORTEP

Read CIF

Create SDT Create CRT Exit Program

Read in Atoms

Acknowledge

Let’s have an example

Ylid Test Structure