Hi Falgun,
You're trying to guess commands. Maybe reading is a better option. Try
'help dist'. From there you'd find that
dist atom1, atom2
would do the job.
Alternatively, to draw arbitrary lines between coordinates, you can use CGO:
cmd.load_cgo([ 9.0, 13.668, -9.582, 5.011, 13.668, -9.582, 5.011, 0.2,
1,1,0, 1,0,1 ], "spring")
But then again, you can even add pseudoatoms to your system based on
the centers of mass of groups of atoms and use these for distances.
If you feel you must have springs, you'll have to do it with CGO and
wil have to do programming. For arrows you can try to dig up posts of
mine from the user list. I've sent python code for drawing these
several times.
Hope it helps,
Tsjerk
On Fri, Mar 13, 2009 at 3:20 PM, Falgun Shah <fhs...@olemiss.edu> wrote:
> 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 <fhs...@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 <war...@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: falgunhs...@gmail.com [mailto:falgunhs...@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 <war...@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:fhs...@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: fhs...@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: fhs...@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: fhs...@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: fhs...@olemiss.edu
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
