Daylight Summer School 1998, July 28-30, St. John's College, Santa Fe, NM
Daylight Worksheet - Structural, Non-Structural, Mixture and Reaction searching with xvmerlin
xvmerlin is an XView interface to Daylight Databases which have
been loaded into Merlin Pools. Day 2 will describe the administration
of Merlin Pools. For today, databases have already been loaded for
you. One difficulty when first trying to use xvmerlin, is
proper usage of the three mouse buttons. By default the right
mouse button enables you to see and select from popup menus. The
left mouse button allows for selections from popup windows
and to activate popup windows. The middle mouse button will
display the full data tree for a given structure.
Structural Searching using xvmerlin
- Start xvmerlin and open a database
xvmerlin(Sun system) or
xvmerlin4d(SGI system) to start merlin client . With the right mouse button select
Open Database drag mouse to
right and select
Superstructure Search-Finding structures in database which contain a given substructure
Your results from your search are now stored in a hitlist which you
can recall later. Select
- Use right mouse button on the
SMILES column and make
Select Search type (try both SMILES and SMARTS), Try Grins utility
to draw in a structure or type in SMILES or SMARTS. Select
which type of Action, e.g. Make new hitlist. When ready hit
- Save hitlist by using the right mouse button and select the
Hitlist menu from the xvmerlin window, Select
Hitlist with the left mouse
button or select the menu item
Set all hit to return
to searching the whole database.
Substructure Search-Finding structures embedded with given structure
Similarity Search-Finding structures which are similar to a given structure
- In the "Merlin search control panel" window change the
"Look for" option to find structures embedded with given structure.
Try a different Action (e.g. "remove matches from hitlist"). Make a new hitlist by combining the results with the hitlist
from your Superstructure search. Select
Hitlist menu. Your hitlist will now
contain all structures from medchem98 which contain the substructure
requested in the Superstructure search and all medchem98 compounds which
are not embedded within the structure specified in the Substructure
- Try out various union/intersections of hitlists and use
the left mouse button to select the
column for a popup window with a larger view of the structures.
- Select the
Display menu in the xvmerlin
window and try out the Merlin keypad. Make selections with
the left mouse button.
- Perform a taniomoto similarity search using xvmerlin
- Perform a tversky similarity search using xvmerlin
- Generate a similarity column in the xvmerlin window by pressing the
middle mouse button just to the right of the SMILES column.
- Use the right most mouse button on the smilarity column to select
a different datatype. Create a column containing the LogP star datatype.
- Find all structures which have measured LogP values between 1 and 3
and sort the results.
- Open the mix98demo database
- Search for a component in a dot-disconnected mixture,e.g. 'CCC(C)C(N)C(O)NC(CC(O)O)C(O)NC(CC(C)C)C(O)O'
- Search for Tri-peptides mixtures which have at least one aspartic acid. Monomer for aspartic acid is "Asp"
- Open the ccr972demo database
- Search for all reactions with a reactant of your choice (e.g. 'COC(OC)N(C)C')
- Find a set of reactions that are in the same XOR cluster, is it obvious why they are grouped together?
- Find all structures in the spresi95demo database which contain
phenyl amine, have synthetic references
and have a melting point <= 200.
- Find all structures in the wdi98demo database which have
both a Hydrogen bond doner and a halogen connected to an
atom three bonds away and has diuretic activity. ([O,N;!H0;R0]~[a,A]~[a,A]~[a,A]-[Cl,Br,F,I]).
Daylight Chemical Information Systems Inc.