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 <[email protected]> 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 <[email protected]> wrote:
>
>> Your message is confusing – did it work or not?
>>
>>
>>
>> All we have at present are dashed lines – no springs or no arrows.
>>
>>
>>
>>
>> ------------------------------
>>
>> *From:* [email protected] [mailto:[email protected]] *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 <[email protected]>
>> 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:[email protected]]
>> *Sent:* Wednesday, March 04, 2009 8:46 AM
>> *To:* [email protected]
>> *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: [email protected]
>>
>>
>>
>>
>> --
>> 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: [email protected]
>>
>
>
>
> --
> 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: [email protected]
>
--
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: [email protected]
