Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
Photo
- - - - -

Importing Custom Ligands in Pymol


  • Please log in to reply
2 replies to this topic

#1 DavidEckert

DavidEckert

    member

  • Members
  • Pip
  • 2 posts
0
Neutral

Posted 18 September 2013 - 05:42 AM

I'm currently working on a fourth year molecular biology project and I'm having some trouble importing files into pymol. What I want to do is create a custom ligand and import it into pymol with a pdb protein file. So far, I have tried using marvin sketch to create the molecule and trying to import the file via different file types (pdb,cube,mol ect...). Pymol either crashes or it makes the original protein disappear. Does anyone have any suggestions? Should I maybe use a new program altogether?

 

David

 

 



#2 jerryshelly1

jerryshelly1

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 328 posts
29
Excellent

Posted 18 September 2013 - 12:20 PM

When you import your new ligand and your orignal protein dissappers, does it still list the original protein in the right side bar? It could be that you are entering a very small ligand (compared to your protein) and it blowing out your protein from view.  I would try centering on your protein (easily done in protein drop down menu) and then moving your ligand to your protein.

 

Depending on the complexity of your ligand, you can easily draw it within Pymol.  I have found that for some projects, this is much easier.

 

I think the issue is that when you upload your ligand, your protein gets pushed out of frame.

 

Let me know if that works.



#3 DavidEckert

DavidEckert

    member

  • Members
  • Pip
  • 2 posts
0
Neutral

Posted 18 September 2013 - 03:35 PM

Thanks for the suggestion, I finally found the protein. The pymol zoom function and viewing model can be a real irritation.

 

David






Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.