Dear pymol users

Is it possible to draw distance between two coordinates.  i want to measure distance between Center of mass of two atoms  {13.668 -9.582 5.011} and atom 20224 {13.668 -9.582 5.011}

i tried like this: dist spring, {13.668 -9.582 5.011},{13.668 -9.582 5.011}, label=0
but it did not work.
Please let me know how to do it.

thanks

On Mon, Mar 9, 2009 at 5:19 PM, Falgun Shah <fhshah@olemiss.edu> wrote:
Dear Dr. warren
it did work the way you suggested , however i wanted spring instead of dashed lines. Thanks for your help


On Mon, Mar 9, 2009 at 5:04 PM, Warren DeLano <warren@delsci.com> wrote:

Your message is confusing – did it work or not?

 

All we have at present are dashed lines – no springs or no arrows.

 

 


From: falgunhshah@gmail.com [mailto:falgunhshah@gmail.com] On Behalf Of Falgun Shah
Sent: Monday, March 09, 2009 3:02 PM
To: Warren DeLano
Subject: Re: [PyMOL] drawing a spring/arrow with pymol

 

Dear Dr. Warren

I executed  the command as follows: dist spring, resi 580 and name ca, resi 7056, lable=0

i was able to draw a dotted line between two points.Actually, I need a spring with the coil inside. I was performing smd simulation and i just want to show spring in the applied force direction. I am a fan of the graphics in Pymol. if i am able to execute the spring between two points it would be wonderful.  Am i making some mistake in executing command. Please let me know solution to this. or any other way possible.

Thanks

On Wed, Mar 4, 2009 at 12:22 PM, Warren DeLano <warren@delsci.com> wrote:

Falgun,

 

We don’t have an arrow primitive, but you can use the distance command to connect two atoms:

 

dist spring, selection1, selection2, label=0

 

for example:

 

fragment val

 

dist spring, val////CG1, val////CG2, label=0

 

Cheers,

Warren

 

 


From: Falgun Shah [mailto:fhshah@olemiss.edu]
Sent: Wednesday, March 04, 2009 8:46 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] drawing a spring/arrow with pymol

 

Dear pymol users

I am running SMD simulation. I want to draw arrow/spring to display direction of pulling of my ligand. i know it is possible with VMD. but i am more attracted to graphics in Pymol. is it some way i can draw arrow or spring connecting two atoms. please let me know



--
Falgun H shah
PhD candidate (3rd year)
Department of Medicinal Chemistry
2028, Natural Product Center
University of Mississippi

Ph No: 6629151286(O)
          662 801 5667(M)
email: fhshah@olemiss.edu




--
Falgun H shah
PhD candidate (3rd year)
Department of Medicinal Chemistry
2028, Natural Product Center
University of Mississippi

Ph No: 6629151286(O)
          662 801 5667(M)
email: fhshah@olemiss.edu




--
Falgun H shah
PhD candidate (3rd year)
Department of Medicinal Chemistry
2028, Natural Product Center
University of Mississippi

Ph No: 6629151286(O)
          662 801 5667(M)
email: fhshah@olemiss.edu



--
Falgun H shah
PhD candidate (3rd year)
Department of Medicinal Chemistry
2028, Natural Product Center
University of Mississippi

Ph No: 6629151286(O)
          662 801 5667(M)
email: fhshah@olemiss.edu