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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