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@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@cgl.ucsf.edu> On Thu, Aug 18, 2011 at 7:48 PM, Eric Pettersen <pett@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@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@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@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@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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