Re: [Jmol-users] Electron density in X-PLOR format and CCP4 format SUCCESS!

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Eric, OK, I agree. We are very close. You can see that there is a slight
alignment error  if you set the cutoff to 4.0. There appears to be needed a
0.5 grid adjustment in ONE DIRECTION ONLY.

This, of course, is disturbing. However, before I hack this and then find
out it's a data source error, I'd appreciate some testing on your part. I
need convincing that:

a) this is true for other CCP4 files you check
b) this is true or not true for XPLOR files (I think it is NOT true for the
one
    at the pymol tutorial)
c) with CCP4 files that have different maps, mapr, or mapc parameters,
    it is still true (and what direction is now off?)
d) map files from a different server produce the same error

And if that's the case - that it is generally true, then we need to ask the
people at Scripps or Uppsula  why that would be the case.

What I do know is:

a) The overall scaling is perfect. This is an offset problem, not a scaling
issue
b) Jmol reliably puts the origin in the right place for other file types -
this is something unique to MRC, CCP4, or XPLOR
c) It does not appear to be a problem with the 1w2i XPLOR example at the
pymol tutorial site.
d) Jmol is running both XPLOR and CCP4 files through the same base reader,
so we need to know if it is a problem common to one or the other or both.

What you can do:

With the version of Jmol I just uploaded into
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip you can add the
CENTER parameter. This will offset the model in crystallographic unit cell
"unit vector" coordinates:

load 1w2i.pdb;display TYR
 isosurface within 2.0 {TYR} cutoff 3.0 color yellow  center {0 0 0.5}
"1w2i.xplor" mesh nofill

So please experiment with that today and find out what works empirically.

Bob

On Mon, Jan 18, 2010 at 8:00 AM, Eric Martz <mar...@ya...> wrote:

> Dear Bob,
>
> You've made FANTASTIC progress! Really exciting!
>
> For 11.9.20_dev Jan 16 18:11
>
> It appears to me that the map is slightly offset from the atoms, in the
> negative X direction -- look at the red oxygens sticking up and down in this
> snapshot (axes are visible):
> http://www.umass.edu/molvis/tests/jmol-edm-test3/3hyd_jmol.png
>
> Compare with same in PyMOL:
> http://www.umass.edu/molvis/tests/jmol-edm-test3/3hyd_pymol.png
>
> Secondly, the PyMOL map is contoured at 1.0 sigma. The Jmol map appears
> similar -- is the default 1.0 sigma? Is the "cutoff" reported as 1.48 the
> sigma value? How do I set the sigma? (Please remember, the script manual is
> unavailable at the moment.)
>
> By the way, I've made every map I've mentioned on this list downloadable at
> the URL I gave in the email -- download links are in a big pink box. No
> matter now, we can all use the easily available ccp4 maps from
> http://eds.bmc.uu.se/eds/ (just wanted you to know I tried to make it easy
> for you to get the files).
>
> -Eric
>
>
> > From: Robert Hanson <ha...@st...>
> > Subject: [Jmol-users] Electron density in X-PLOR format and CCP4 format
> SUCCESS!
> > To: jmo...@li...
> > Date: Sunday, January 17, 2010, 7:58 PM
> > OK, Eric, I found a couple of map files.
> > Everything looks perfect to me, but of course it needs
> > testing. See
> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip.
> > Jmol 11.9.20_dev
> >
> >
> > WOW, I have to say, this is exciting. I want to learn more
> > about electron density maps!  Jmol loads this one
> > instantly:
> >
> > isosurface  color yellow within 2.0 {*}
> > "c:/temp/3hyd_map.ccp4" mesh nofill;
> >
> > reading isosurface data from c:/temp/3hyd_map.ccp4
> > FileManager opening c:\temp\3hyd_map.ccp4
> > data file type was determined to be MRC
> >
> > FileManager opening c:\temp\3hyd_map.ccp4
> > MRC header: mode: 2
> > MRC header: dmin,dmax,dmean:
> > -1.1890318,4.998787,-0.014114891
> >
> > MRC header: ispg,nsymbt: 5,0
> > MRC header: rms: 0.74718976
> > MRC header: labels: 1
> > Created by MAPMAN V. 080625/7.8.5 at Fri Jan 15 04:34:50
> > 2010 for A. Nonymous
> > MRC header: bytes read: 1024
> >
> >
> > MRC/Jmol interpretation:
> >
> > MRC/Jmol cutoff set to (dmean + 2*rms) = 1.4802647
> > grid parameters: nx,ny,nz: 38,90,55
> > grid parameters: nxStart,nyStart,nzStart: -11,-6,-11
> > grid parameters: mx,my,mz: 144,16,56
> >
> > grid parameters: a,b,c,alpha,beta,gamma:
> > 49.475,4.8375,19.4375,90.0,96.65,90.0
> > grid parameters: mapc,mapr,maps: 2,1,3
> > grid parameters: originX,Y,Z: 0.0,0.0,0.0
> > grid header: a,b,c,alpha,beta,gamma:
> > 49.475,4.8375,19.4375,90.0,96.65,90.0
> >
> > Jmol unit cell vectors:
> >     a: (0.34357637, 0.0, 0.0)
> >     b: (-1.3215866E-8, 0.30234376, 0.0)
> >     c: (-0.040195342, -1.692914E-8, 0.34476298)
> > Jmol origin in unit cell coordinates: (-3.3371913,
> > -1.8140624, -3.7923927)
> >
> > Jmol use   isosurface OFFSET {x y z}   if you want to
> > shift it.
> > Jmol origin in slow-to-fast system: (-1.8140624,
> > -3.3371913, -3.7923927)
> >
> > voxel grid origin:(-1.8140624, -3.3371913, -3.7923927)
> > voxel grid count/vector:55 -0.040195342 -1.692914E-8
> > 0.34476298
> >
> > voxel grid count/vector:90 0.34357637 0.0 0.0
> > voxel grid count/vector:38 -1.3215866E-8 0.30234376 0.0
> > JVXL read: 55 x 90 x 38 data points
> > VolumeFileReader reading data progressively
> > boundbox corners {-0.7172928 -0.3137546 -1.3790519}
> > {25.194487 5.128433 12.066704}
> >
> > VolumeFileReader closing file: data min/max/mean =
> > -1.1890318, 4.998787, -0.01760154
> > isosurface1 created with cutoff = 1.4802647 ; number of
> > isosurfaces = 1
> >
> >
> > On Sun, Jan 17, 2010 at 12:26 PM, Robert Hanson <ha...@st...>
> > wrote:
> >
> > I'll need the xplor file. Not
> > finding that...
> >
> >
> > On Sun, Jan 17, 2010 at 11:50 AM, Eric Martz <mar...@ya...>
> > wrote:
> >
> > I
> > found instructions here
> >
> > http://www.ucl.ac.uk/~rmhasek/pymol.html<http://www.ucl.ac.uk/%7Ermhasek/pymol.html>
> >
> >
> >
> > for using a program called mapman to convert ccp4 electron
> > density maps to x-plor format. I think I did that, but my
> > results in Jmol 11.9.19 were unsatisfactory. You can see
> > snapshots and download the map and other files here:
> >
> >
> >
> >
> >
> > http://www.umass.edu/molvis/tests/jmol-edm-test2/
> >
> >
> >
> > Comments? Help?
> >
> >
> >
> > -Eric
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> >
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> >
> >
> > --
> > 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
> >
> >
> >
> >
> > --
> > 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
> >
> >
> > -----Inline Attachment Follows-----
> >
> >
> ------------------------------------------------------------------------------
> > Throughout its 18-year history, RSA Conference consistently
> > attracts the
> > world's best and brightest in the field, creating
> > opportunities for Conference
> > attendees to learn about information security's most
> > important issues through
> > interactions with peers, luminaries and emerging and
> > established companies.
> > http://p.sf.net/sfu/rsaconf-dev2dev
> > -----Inline Attachment Follows-----
> >
> > _______________________________________________
> > Jmol-users mailing list
> > Jmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for
> Conference
> attendees to learn about information security's most important issues
> through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>

-- 
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

Re: [Jmol-users] Electron density in X-PLOR format and CCP4 format SUCCESS!

An interactive viewer for three-dimensional chemical structures.

Re: [Jmol-users] Electron density in X-PLOR format and CCP4 format SUCCESS!