Subject: Summary of "How to link atoms in SYBYL?"

From: Zhang Hongyu <[email-masked]>
Date: Mon, 20 Mar 1995 14:21:18 +0800 (SST)

Hi, everyone,

Thanks for your helpful advices to my query on atom connection in sybyl.
Here is a summary. 

My original question is
> 
> Dear netters,
> 
> 	Here is a question about SYBYL.
> 
> 	When I use SYBYL to read a molecular coordinate file, such as PDB
> file, sometimes many peptide atoms were discret in the screen, without
> bond linked to each other. I know there is a menu in QUANTA able to link
> them together with algorithms such as distance search. I wonder if there
> is any similar function in SYBYL.
> 	Thanks for your helpful advices.
> 
> Henry H. Zhang
> 

===================================================================

From: "Robert F. Setlik" <[email-masked]>

Check to see if you are using the correct dictionary.  I know that
if, for example, you bring in a DNA PDB file while in the PROTEIN
dictionary, the residues will not be connected.  Also if the distance
between the atoms of the peptide bond are abnormally distant, SYBYL
may not put in the bond.   However if you are bringing in a protein
PDB with the PROTEIN dictionary, which is the default,  the individual
amino acids will be connected automatically.

Hope this helps!!

Rob Setlik 

_______________________________________________________________

Robert F. Setlik
Biophysics Department,
Roswell Park Cancer Institute,
Buffalo, NY
14263
CCC 218

Phone (716) 845-3048 (Lab)
Fax:  (716) 845-8906
Email: [email-masked]

Member of the 'Buffalo Bill's four time Superbowl loss support
and crisis group'.
_______________________________________________________________

===============================================================

From: Emil Marcus <[email-masked]>

When you bring in the PDB file, do not CENTER !   Than use the CRYSIN functionality.
Emil

Emil Marcus
Department of Biophysics
University at Buffalo
[email-masked]

===============================================================

From: [email-masked] (James F. Blake)

Henry,

  I wrote a simple SPL script to do what you want.  Save the below
script as "fixbonds.spl" and then type "take fixbonds.spl" at the
"Sybyl>" prompt.  After you read a molecule in, you can type the command
"fixbonds m1" for a molecule in molecular area m1 and it will connect the
bonds.

  Jim Blake ([email-masked])

( ! I am sorry to omit the original code FOR COPYRIGHT REASON, if anyone
want the code, please directly contact with Mr. Jim Blake )

=====================================================================

From: E.E.Moret <[email-masked]>

The QUANTA comparable distance connectivity search can be found
under BUILD/EDIT CRYSTALS in menumode or CRYSIN CONNECT in command mode.

Regards
Ed Moret
-------------------------------------------------------------------------
E.E. Moret	(@more@)			    [email-masked]
Computational Medicinal Chemistry/Department of Pharmaceutical Chemistry
Faculty of Pharmacy/Utrecht University/the Netherlands
Telephone	(31-30)536979/536958        Facsimile      (31-30)516674
-------------------------------------------------------------------------

=====================================================================

From: [email-masked] (Ed Jaeger)

Henry,

I believe that there is a tailor setting for the Brookhaven which
allows one to adjust the distance criteria used to identifying
adjacent residues.  Just look under 'tailor set brookhaven' for some
leads.

Ed Jaeger      3-Dimensional Pharmaceuticals, Inc.	      ph:610-458-6052
[email-masked] 665 Stockton Drive, Suite 104, Exton, PA 19341 fx:610-458-8249