[Chimera-users] Fwd: Showing more than a single centroid trace

Sat Aug 20 07:59:48 PDT 2011

There is still a problem that had previously escaped my attention.
I.e., after the centroid sequence is obtained for model 0 and residue
1, I run the movie for model 1 and residue 2. That's OK, however the
second series of centroids starts with progressive number where the
first one had ended plus one (if the first series was 1-250, the
second series starts from 251). This means that the first part of
centroids for model 1 (corresponding to the centroids for model 0,
i.e., 250) is not shown.

I used

define centroid radius ... color ... #modelnumber:residuename & :residuenumber

where the residuename is the same for the two series of centroids.

Can the command be modified so that both complete series of centroids is shown?

I am using

 chimera production version 1.5.3 (build 33475) 2011-05-24 17:23:26 GMT

on Debian i386 (I found this more stable than on Debian amd64 with
GTX-580 as the sole graphic cards)

Thanks
francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Thu, Aug 18, 2011 at 8:08 PM
Subject: Re: [Chimera-users] Showing more than a single centroid trace
To: Eric Pettersen <pett at cgl.ucsf.edu>

On Thu, Aug 18, 2011 at 7:48 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Try selecting just the one ligand first with this:
> sel #0:residuename & #0:residuenumber
> then it and the environment around it with:
> sel sel z<5
> --Eric

That works fine, thank you very much

francesco

>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> On Aug 18, 2011, at 10:36 AM, Francesco Pietra wrote:
>
> On Thu, Aug 18, 2011 at 7:07 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> HI Francesco,
>
> Just put the model number wherever you need it, with no space before residue
> name or number, maybe something like:
>
> sel #0:residuename & #0:residuenumber z<5
>
> For me  that works between the three ligands only. I.e, with a large
> z<20, all the three residues are highlighted, while with z<3 only the
> residue with the specified residue number is highlighted. The number
> of atoms at the bottom line correspond. For example, with z<20,  6
> atoms, 3 bonds (three diatomic molecules)
>
> francesco
>
>
> Elaine
>
> On Aug 18, 2011, at 9:46 AM, Francesco Pietra wrote:
>
> Hi Elaine:
>
> Thanks a lot. Could you also help me as how to find the environment of
>
> the moved ligand, when there are three of them with the same residue
>
> number?
>
> While define centroid works nicely with:
>
> define centroid radius# color # :residuename & :residuenumber
>
> sel #modelnumber :residuename & :residuenumber z<#
>
> does not. Could the command be modified to refer to only one of the
> residues?
>
> Thanks
>
> francesco
>
> On Wed, Aug 17, 2011 at 7:34 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> Hi Francesco,
>
> If your movies are different model numbers, you can put model number before
> residue name, for example:
>
> #0:hem
>
> You can see what models you have in the Model Panel (under Favorites in
> menu).
>
> Elaine
>
> On Aug 17, 2011, at 7:11 AM, Francesco Pietra wrote:
>
> Hi Elaine;
>
> I selected with line command the molecule that was giving the centroid
>
> sequence. I was interested in the surroundings of that biatomic
>
> molecule at various frame numbers. What I said, is that this is
>
> possible only for the first movie. On subsequent movies, superimposed
>
> to the first one, the line command always refers to that molecule of
>
> the first movie.
>
> francesco
>
> On Tue, Aug 16, 2011 at 7:38 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> Hi Francesco,
>
> You cannot select centroid objects with a command -- they do not have
> residue or atom names.  You can only select them by clicking their lines in
> the Axes/Planes/Centroids dialog, or by Ctrl-clicking on them in the Chimera
> graphics window.
>
> Elaine
>
> On Aug 16, 2011, at 9:36 AM, Francesco Pietra wrote:
>
> Hi Elaine:
>
> I'll try your advice as soon as possible. However, turning mode1 out
>
> of view in model window while playing movie for model 1, the centroid
>
> for mode1 is still seen above model 0 and the trace for centroid for
>
> model 0 . What I could not do was to select the centroid for model 1,
>
> in order to highlight it. Command "sel :residuename" always selected
>
> the centroid for model 0.
>
> francesco
>
> On Tue, Aug 16, 2011 at 5:51 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> Hi Francesco,
>
> I'm not sure I understand what you are asking.  Maybe you are saying that
> when you hide a model, the centroid is also hidden?
>
> Instead of hiding the model with the Model Panel "Shown" checkbox or command
> "~modeldisplay", which hides everything in the model, you can undisplay the
> protein parts and leave the centroid displayed.  For example, if I had
> protein models #0 and #1 and also centroids for each of those, I could
> undisplay the protein part only of #0:
>
> ~display #0
>
> ~ribbon #0
>
> ~surf #0
>
> (commands to undisplay atoms/bonds, ribbon, and molecular surface of model
> #0).  Then, you would have the protein #1 plus the centroids of both #0 and
> #1 displayed.  I hope this helps,
>
> Elaine
>
> ----------
>
> Elaine C. Meng, Ph.D.
>
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>
> Department of Pharmaceutical Chemistry
>
> University of California, San Francisco
>
> On Aug 15, 2011, at 11:36 PM, Francesco Pietra wrote:
>
> Hello:
>
> I would like to show several centroid traces for model 0, 1, 2, ..
>
> Actually, it is the same model, differing, in the movies, for the
>
> protein fluctuations.
>
> What I did, was to superimpose movie for model 1 to the already done
>
> movie for model 0, hiding the protein for model 1 and choosing a
>
> different color for the centroid. Doing that, the instant position of
>
> the centroid can only be color-highlighted for model 0.
>
> I wonder whether there is a better procedure to show the various
>
> centroid traces above a single protein model.
>
> thanks
>
> francesco pietra
>
>
>
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