From: Warren D. <wa...@de...> - 2009-03-04 18:22:59
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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:fh...@ol...] Sent: Wednesday, March 04, 2009 8:46 AM To: pym...@li... 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: fh...@ol... |
From: Falgun S. <fh...@ol...> - 2009-03-13 14:20:46
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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 <fh...@ol...> 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 <wa...@de...> wrote: > >> Your message is confusing – did it work or not? >> >> >> >> All we have at present are dashed lines – no springs or no arrows. >> >> >> >> >> ------------------------------ >> >> *From:* fal...@gm... [mailto:fal...@gm...] *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 <wa...@de...> >> 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:fh...@ol...] >> *Sent:* Wednesday, March 04, 2009 8:46 AM >> *To:* pym...@li... >> *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: fh...@ol... >> >> >> >> >> -- >> 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: fh...@ol... >> > > > > -- > 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: fh...@ol... > -- 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: fh...@ol... |
From: Tsjerk W. <ts...@gm...> - 2009-03-13 15:44:24
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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 <fh...@ol...> 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 <fh...@ol...> 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 <wa...@de...> wrote: >>> >>> Your message is confusing – did it work or not? >>> >>> >>> >>> All we have at present are dashed lines – no springs or no arrows. >>> >>> >>> >>> >>> >>> ________________________________ >>> >>> From: fal...@gm... [mailto:fal...@gm...] 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 <wa...@de...> 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:fh...@ol...] >>> Sent: Wednesday, March 04, 2009 8:46 AM >>> To: pym...@li... >>> 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: fh...@ol... >>> >>> >>> -- >>> 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: fh...@ol... >> >> >> -- >> 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: fh...@ol... > > > > -- > 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: fh...@ol... > > ------------------------------------------------------------------------------ > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are > powering Web 2.0 with engaging, cross-platform capabilities. Quickly and > easily build your RIAs with Flex Builder, the Eclipse(TM)based development > software that enables intelligent coding and step-through debugging. > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- 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 |
From: Oganesyan, V. <OganesyanV@MedImmune.com> - 2009-03-04 22:41:52
|
Colleagues, If the PDB file contains only Ca atoms and PyMOL shows them as non-bonded atoms what one should do to display them as a ribbon? The 1rh2 entry is one of them. Thank you. _______ Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. |