Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Dear James. I found the hollow script and/or Castp quite useful for this. There exist also a program called surfplot, from Roman Laskowski again. It is integrated in the pdbsum interface and creates ther surfaces. You may look there for examples. Another possibility is Voidoo from Uppsala.

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Dear Christian, thank you for infromation- I'll examine this software. In particular I'm looking for possible modules for pymol because as I've found previously it's a good visualisation of the surfaces wich have been already included in PyMol. 2012/6/28 Christian Roth

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

I've obtained accademical licence on LigProt and I found that this softwatre is most handfull in the 2d analysis of protein-ligand interactions. Is it possible to integrate it into pymol what have been done in case of Pose view ? ) By the way does anybody know any another intresting software or

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

By the way in some papers I've seen 2D schematic diagrams of the protein-ligand interactions. The exapmle of such maps could be found here http://ars.els-cdn.com.sci-hub.org/content/image/1-s2.0-S0005273610001707-gr4.jpg Could you tell me examples of software wich could produce such maps?

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Hi James, the program you can use for this is ligplot from Roman Laskowski at the EBI. the solvent accessability shading is done with the help of naccess. Best Regards Christian Am Dienstag 26 Juni 2012 08:07:07 schrieben Sie: By the way in some papers I've seen 2D schematic diagrams of

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Hi Christian! As I understood that LigPlot is not free for accademical ussage isnt? By the way in that paper http://onlinelibrary.wiley.com.sci-hub.org/doi/10.1002/minf.201000167/pdf there is exhaustive comparison of three different packages for such 2D diagram generation. Have anybody used such

[PyMOL] Visualisation of protein-ligand interactions in pymol

Hi James, LigPlot is free for academic users. You just have to verify that you are a academic user. MOE does a simimlar representiation but is definitely not free. Christian -- Live Security Virtual Conference

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Christian, Also I've found the same software- pose view (in that article I've also found link on it). Its very friendly but I've noticed some erorrs during representation of the non-covalent contacts partly in case of the vdw interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw but

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Hi all, I thought it would be nice to run such tools directly from PyMOL. So there is a PoseView wrapper on the PyMOLWiki now: http://pymolwiki.org/index.php/PoseView A LigPlot wrapper may follow... Cheers, Thomas On 06/26/2012 10:13 AM, James Starlight wrote: Christian, Also I've found

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Thomas, Its really great ) Could you tell me if you find a possible way to take into account burried water from the protein interiour in the Pose View protein-ligand interaction 2D plots ? Most of my proteins consist of such internal water ( like a het atoms in the protein.pdb ) but pose view

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Hi James, hm, looks like PoseView ignores all water molecules :( Have you tried LigPlot? It has a -w option to include waters. Cheers, Thomas On 06/26/2012 05:11 PM, James Starlight wrote: Thomas, Its really great ) Could you tell me if you find a possible way to take into account

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

I'm still waiting for accademical license on lig prot. By the way it's very strange that PoseView have not been accompanied with 'internal water detector' ;) i've sent the letter to developers with this question and hope they can help James 2012/6/26 Thomas Holder spel...@users.sourceforge.net

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Thomas, thanks this works perfect. Jason, I've tested this script on my system ( this is the membrane protein inserted in the bilayer surrounded by two water layers ( up and down ). During simulation individual water mollecules move into the protein interiour ( in that case protein like a

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

James, 1) I want to visualise individual water mollecules wich have moved to the protein interiour during my MD run. How I could hide all solvent water and visualise only those water wich are within defined cutoff distance from the protein ? You can find buried waters with this script:

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Hi James, [...] Is there any possible way to merge polar interactions with the protein structures to one object ? yes, you can put them in the same group object. This will show them in the same slot in group mode. http://pymolwiki.org/index.php/Group Cheers, Thomas -- Thomas Holder MPI