VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 29 2019 - 12:55:54 CDT

Hi,
  If you work through the VMD tutorials, you can learn how to align
trajectory frames. You can use the draw multiple frames feature
to superimpose the aligned frames on top of each other for direct
visual comparison.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 24, 2019 at 07:29:05PM +0530, Charu Sharma (JRF) wrote:
> Sir I want my figure to be superimposed I want to analyze them that what
> is the difference between the pdb file when they are created after
> minimization, heating and production run. So I have make three pdb files
> now the question arises how to merge them in one figure rather to analyze
> single figure?Â
> On Wed, Jul 24, 2019, 19:12 John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Â There are infinite ways of "making a single figure" it is completely
> unclear what the requirements of this "single figure" are, so nobody
> will have much to say to help until you provide far more specific
> details
> about what it is that you hope to accomplish. From your two emails,
> the only things that is clear is that you want one figure as a result,
> but you say nothing about whether you want three images side-by-side,
> superimposed, colored in some particular way, etc. You've got to put
> some real effort into formulating your question and writing a clear
> and understandable email, or nobody will take the time to try
> and answer you.
>
> Best regards,
> Â John Stone
> Â [2]vmd_at_ks.uiuc.edu
>
> On Wed, Jul 24, 2019 at 02:27:31PM +0530, Charu Sharma (JRF) wrote:
> >Â Â Sir there are the steps of simulation where we perform
> minimization, then
> >Â Â heating and then production dynamics.. Like this the pdbÄ*Â file
> that are
> >Â Â generated after each step.. Then I have to merge all three and
> produce
> >Â Â single figure..Ä*
> >Â Â On Wed, Jul 24, 2019, 14:18 Charu Sharma (JRF)
> >Â Â <[1][3]charu.sharma_at_lnmiit.ac.in> wrote:
> >
> >Â Â Â ---------- Forwarded message ---------
> >Â Â Â From: KARISHMA SHARMA <[2][4]18pph003_at_lnmiit.ac.in>
> >Â Â Â Date: Wed, Jul 24, 2019, 13:31
> >Â Â Â Subject:
> >Â Â Â To: Charu Sharma (JRF) <[3][5]charu.sharma_at_lnmiit.ac.in>
> >
> >Â Â Â how to merged single figure of the three PDB files: initial,
> after
> >Â Â Â minimization, after 1ns run simulation, in VMD.
> >Â Â Â KARISHMA SHARMA
> >Â Â Â JRF (JUNIOR RESEARCH FELLOW)
> >Â Â Â PhD SCHOLAR, LNMIIT
> >
> > References
> >
> >Â Â Visible links
> >Â Â 1. mailto:[6]charu.sharma_at_lnmiit.ac.in
> >Â Â 2. mailto:[7]18pph003_at_lnmiit.ac.in
> >Â Â 3. mailto:[8]charu.sharma_at_lnmiit.ac.in
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [9]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> [10]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. mailto:charu.sharma_at_lnmiit.ac.in
> 4. mailto:18pph003_at_lnmiit.ac.in
> 5. mailto:charu.sharma_at_lnmiit.ac.in
> 6. mailto:charu.sharma_at_lnmiit.ac.in
> 7. mailto:18pph003_at_lnmiit.ac.in
> 8. mailto:charu.sharma_at_lnmiit.ac.in
> 9. http://www.ks.uiuc.edu/~johns/
> 10. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/