Re: [Jmol-users] Re : Re: Problem w/ electron dens. maps

[Robert H. <ha...@st...>]

resending -- message was too long for list.


On Tue, Feb 23, 2010 at 9:50 PM, Robert Hanson <ha...@st...> wrote:

>
>
> On Tue, Feb 23, 2010 at 8:05 AM, <pau...@ac...> wrote:
>
>> I don't know if this can be of interest, but the following website
>> displays results from electron microscopy (datas provided by the EM
>> database) using Jmol :
>> http://emnavi.protein.osaka-u.ac.jp/
>>
>> Here is an example with HIV capsids
>> http://emnavi.protein.osaka-u.ac.jp/view.php?id=1155
>>
>>
> oooh, this one is nice! They are using one of the newest features of Jmol
> -- JVXL pmesh triangle files. Excellent!
>
> Bob
>
>

and

OK, progress! Good job, Thomas.

Well, it wouldn't be the first time that we have found errors in other
systems while working on Jmol. Still proud of finding the bug in ORTEP!

Right, so here is where we are:

a) Then I have Jmol working correctly now for MRC/CCP4 files, and Eric
should be telling us soon that all is to his liking, even with the default
of not specifying sigma, since that will go in as sigma=1.0, which is what
he wants, I think.

b) If you can look into the Uppsala problem, that would be great. Unless I'm
way off base there, that needs to be fixed. I just can't see how it can have
essentially the same min, max, and mean as the MRC data from the same server
and not have those reported in the file. Should be pretty easy for them to
check out.

c) That said, the CNS/Xplor format very disappointingly is not designed with
streaming in mind. One of Jmol's newer features is that it never has to
actually load all the volumetric data (the way PyMOL does). It just streams
the data in slice by slice and creates the surface on the fly. This is far
faster and far more memory efficient and allows Jmol now to display huge
surfaces that it never could before.

Well, for that to work, you clearly have to have the cutoff initially set.
But if it comes at the end of a file -- that's fine for reading a file off
the hard drive, but over the web -- where you don't have the equivalent of
"file.seek()" to jump to the end first, get the info, and then come back --
that's just not possible. That's too bad.

So the point is that while I think it's important that that gets fixed, if
it really is in error, fixing that is not going to allow Jmol to read those
files efficiently. I hate to think that we would have to read them twice
just to do the job. I suppose we could do that.... In any case, the MRC/CCP4
files should be scaling properly now.

d) Thomas, if you could look into the electron microscopy business, that
would be great as well.

and

Great. Thanks, Tom.

Sigma -- This all makes good sense. It explains why 2sigma was a better
match to the EM data, which was the original reason I implemented the MRC
format. But it also seems to me to be quite reasonable to just set sigma=1
to be the default and let people who want to display EM data set the sigma
explicitly.

EDS CNS -- Perhaps we could lobby for also including an indication of RMSD
in the header comment.



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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