[Chimera-users] Morph groups of maps?

Oliver Clarke olibclarke at gmail.com
Sat Jan 30 13:44:08 PST 2016

Thanks for the helpful suggestions Elaine! I will look into them and see
where it gets me - I have a feeling I have tried the perframe/scolor idea
in the past without success but I may be misremembering.

One other thing - I'd like a one command way to convert a full atom model
to a Calpha model, keeping the helix/sheet records at the start intact.
This would be very helpful when running morphs of a large protein (where
often I do not need to display sidechains, just ribbon), because it makes
the calculations much faster (e.g. rather than 120,000 atoms I have ~17000
using CAs only). Currently what I do is I delete all the non-CA atoms in
chimera, save the pdb, remove all the TER flags chimera has added between
each CA atom using grep, and then replace the HELIX/SHEET records with
those from the original file (because they get corrupted for some reason in
the process. This works fine but it would be nice to have a one liner in
chimera to handle the same at some point (although I realize it is a pretty
niche functionality and maybe not worth it). (alternatively a "coarse
grained" morph where parameters for each residue only take into account the
CA would accomplish the same thing I guess.)


On Sat, Jan 30, 2016 at 9:23 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Oliver,
> I haven’t tried these things in a situation similar to yours, but some
> initial ideas are:
> (1) use two “vop morph” commands separated by only a semicolon so that (if
> it is possible to run two map-morphs concurrently), they will start at the
> same frame
> (2) use “perframe” (possibly with “alias”) to specify running “scolor"
> zone command(s) at each frame
> I would try those things one at a time, for example, perframe scolor with
> a single vop morph.  Even in that case, I’m not sure it will work.  We may
> be able to come up with better answer or at least a more definite answer of
> whether it is possible next week.  In the meanwhile, these are just some
> things to look into.
> Best,
> 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 Jan 30, 2016, at 10:16 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> > Hello,
> >
> > In a situation where I have maps for two conformations, and I've
> extracted out domain specific maps in both cases, is it possible to run
> morph maps on both groups of maps simultaneously? Or is there any way to
> apply color zone  to the trajectory generated by morph maps? I would like
> to generate a morph map movie where the map is colored by domain throughout
> the morph, and can't figure out how to do so.
> >
> > Cheers,
> > Oli
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