[Chimera-users] Morph with Chimera: how to make visible connection/interaction in Morph

WENHE ZHONG wenhezhong.xmu.edu at gmail.com
Fri Aug 19 05:49:41 PDT 2011

Hi Elaine,

Thank you so much for these suggestions. They all help! I also find that I
could add the interaction lines in Pymol as well.

King regards,

On 18 August 2011 22:08, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Wenhe,
> As Eric mentioned, in some cases the morph does have the metal ion, but not
> the metal complex bonds.  I will file that as another bug report.
> In the meanwhile, however, if that is the problem you can add the metal
> complex bonds yourself.  First display the atoms that might be interacting
> with the metal (example command:  disp ions z<4).  Also, the ribbon hides
> the backbone atoms, so if you want to see the backbone atom exact positions,
> hide ribbon too, maybe the whole ribbon (~ribbon) or just the ribbon near
> the ions (~ribbon ions z<4).  Now that the atoms are shown, there are at
> least two different ways to add the metal complex bonds.
> (A) If you already know exactly which atoms should have lines to the metal,
> you can just make distance measurements from the metal to each of those,
> then hide their labels showing the distance values.  This can be controlled
> in the Distances panel (under Tools... Structure Analysis), set "Labels" to
> "None."
> For how to add distance measurements and change their appearance, see:
> <
> http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances
> >
> - OR -
> (B) you can use Metal Geometry (under Tools... Structure Analysis) to
> identify the possible coordinating atoms and also add the lines.
> <
> http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeom.html
> >
> Example using Metal Geometry:
> I opened PDB 2l4i as model 0, and since it is an NMR model there are
> multiple submodels 0.1-0.10.  I used 0.1 and 0.2 as input to morphing,
> creating a morph trajectory that is model 1.
> In Metal Geometry,
> - I chose #1 MG 500.A MG (model 1, atom name MG, residue 500 in chain A
> also named MG) from the menu of metal ions.
> - clicked on a line in the Coordination Table to choose which atoms are
> considered coordinated
> - clicked the "Create/Update" button to show the metal complex bonds
> Then, when you play the morph trajectory those same bonds will be shown
> throughout regardless of how those atoms move around.
> I hope this helps,
> Elaine
> On Aug 18, 2011, at 11:51 AM, Eric Pettersen wrote:
> > Hi Elaine,
> >       Well if the structures have identical atomic composition, such as
> the models of NMR entry 2L4I, then the ions are retained in the morph.
>  That's not to say that the failure to retain the ion between 2gbp and 2fw0
> isn't a bug, just that there is some chance that Wenhe's morph retains the
> ion.  You should definitely Trac the 2gbp/2fw0 thing so we can work on
> making ion-retention better.  Also, even for 2L4I the metal-complex
> pseudobonds aren't retained so that could be improved too.
> >
> > --Eric
> >
> >                         Eric Pettersen
> >                         UCSF Computer Graphics Lab
> >                         http://www.cgl.ucsf.edu
> >
> > On Aug 18, 2011, at 11:34 AM, Elaine Meng wrote:
> >
> >> Hi Wenhe,
> >> If the morph trajectory includes the metal ion, you could just display
> it and nearby residues with commands something like
> >>
> >> sel #2 & ions
> >> disp #2 & sel z<4
> >>
> >> (in that example the trajectory is model 2).
> >>
> >> If you already see the metal ion and those atoms but no lines between
> them, that is a different issue -- if that's the problem, let us know, and I
> can give more explanation of how to add the lines.
> >>
> >> However, I suspect the morph trajectory does not include the ions.  I
> just tried morphing between two structures that both contain a Ca++ ion,
> 2gbp and 2fw0, but the resulting morph trajectory only included the protein
> part, even if I edited the files first so that the Ca++ had the same residue
> number.
> >>
> >> The morph trajectory is supposed to include the atoms that are in both
> input structures, but for some reason the Ca++ ion is not recognized as
> being the same.  I don't know how easy this would be to fix (I'm not one of
> the programmers), but I will report this as a bug and include your email
> address so that you will receive update messages if anything happens.  Maybe
> somebody else has an idea of how to work around this problem?
> >>
> >> Sorry about that,
> >> 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 18, 2011, at 9:40 AM, WENHE ZHONG wrote:
> >>
> >>> Dear all,
> >>> I would like to show the visible metal-residue interaction during the
> Morph movie. Anyone knows how to do that in Chimera? Thank you.
> >>> King regards,
> >>> Wenhe
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