It is currently Sun Nov 18, 2018 7:58 am

All times are UTC




 Page 1 of 1 [ 3 posts ] 
Author Message
 Post subject: Stereochemistry at ligand setup
PostPosted: Mon Jan 16, 2012 7:05 pm 

Joined: Fri Jan 06, 2012 12:04 pm
Posts: 23
It seems that after processing a racemic ligand the server randomly chooses the stereochemistry for it (and it cannot be later edited!) Is there any possibility to have a selection after uploading/drawing the ligand(s) to define the appropriate stereo bond to be either r, s or racemic? And would it be possible to automagically do do all the stereoisomers for the docking?


Offline
 Profile  
 
 Post subject: Re: Stereochemistry at ligand setup
PostPosted: Mon Jan 16, 2012 7:41 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
If you use chiral bonds in drawing ("Single up" and "Single down" in the top left dropdown menu) it should work well. Some enantiomer-making automagic sounds good, I put this task into our todo list :)


Offline
 Profile  
 
 Post subject: Re: Stereochemistry at ligand setup
PostPosted: Mon Jan 16, 2012 8:49 pm 

Joined: Fri Jan 06, 2012 12:04 pm
Posts: 23
Yes, I figured it out after some serious hair pulling. The problem was that when I made a sdf file with chembio-office/Chemsketch, the S's and R's were not the same in the program than in your software :D. It's a feature of those programs, not yours I think. Now I have understood how to draw them "correctly" before doing the sdf.
And when drawing them on the server I always remember to select view --> stereo R/S-labels --> all before clicking ok :)

Anyway -the racemic docking possibility is a must!


Offline
 Profile  
 
Display posts from previous:  Sort by  
 Page 1 of 1 [ 3 posts ] 

All times are UTC


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  

cron