Wow, you are good, Eric!

You should be all set with Jmol 11.8.24 or 12.0.RC9, which I will upload later this morning.

>>PROBLEM 1: Missing AU's in Biomolecule

I naively assumed that the identity operation would always be listed first. That's not the case in these, so it was skipping the first operation. Jmol does always apply "x,y,z" as the FIRST symmetry operation - ensuring that when you use

select symop=1

or

color property symop

the first symmerty operation is the set of coordinates actually in the file.

>> PROBLEM 1b: Similarly, although 2tmv specifies 49 copies in REMARK 350, symop selection works only for 1-45. (I can't easily count the AU's here!)

Oooh, you are good! This was the issue that some biomolecules are not crystallographic! The tobacco mozaic virus example is a rod of infinite length. In that case, the symmetry operations correspond to a spiral of arbitrary helical angle. Very interesting! Jmol assigns a Jones-Faithful (x,y,z+1/2) operation name, but that is not actually appropriate in this case. So some of these repeated, and the count was off. A simple fix. Just don't take the J-F operation labels too seriously, and I have to check on whether compare symop=n works in this case.

>>PROBLEM 2: I can select a given AU in the biomolecule assembly

This should not be a problem. Note also that there is no "symop=0". Symop starts with 1.

>>PROBLEM 3: Similarly, I can "color backbone brown" after "select symop=N" for N=2-45 with 2tmv, but not for N=1.

See problem 1.

color symop request:

Just use

color property symop

Note there that in the color command you need "property" because there is no "symop" color scheme like there is for molecules, etc. Same, for example, with:

color property model

A bit of a nuance...


Bob


On Wed, Apr 28, 2010 at 2:24 AM, Eric Martz <emartz@microbio.umass.edu> wrote:
Dear Bob,

I find the following apparent bugs in 12.0.RC8:

PROBLEM 1: Missing AU's in Biomolecule

load 3a69.pdb filter "biomolecule 1"

produces an assembly of 10 asymmetric units instead of the 11
specified in REMARK 350.
In contrast, RCSB's Biological Assembly and the product of MakeMultimer.py
(http://watcut.uwaterloo.ca/cgi-bin/makemultimer/) contain the 11
specified AU's.

Similarly, although 2tmv specifies 49 copies in REMARK 350, symop
selection works only for 1-45. (I can't easily count the AU's here!)

PROBLEM 2

I can select a given AU in the biomolecule assembly with e.g.

select symop=1

After such selection

color red
color cartoon green

work in 3a69 for symop=2 to symop=10 (there is no symop=0 and no symop=11) but

color cartoon green

does not work for symop=1.

Similarly, I can "color backbone brown" after "select symop=N" for
N=2-45 with 2tmv, but not for N=1.

Neither of the above problems occurs with 1hho, where REMARK 350
specifies only two AU's in the biomolecule.

---------

Finally, I'd like to suggest that

color symop

work like "color chain", assigning a different color to each symop number.

Thanks, -Eric



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Robert M. Hanson
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St. Olaf College
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If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900