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Hi Mike,<br>
<br>
The reason the unit cell for the solvent-only model looks different
is because the asymmetric units are positioned so that their geometric
center (i.e. unweighted average atom position) lies within the unit
cell box. If you remove the non-solvent that changes the geometric
center quite a bit for this structure and the translations to put the
centers of the asymmetric units in the unit cell come out differently
than for the all-atom model.<br>
<br>
My understanding of the term "asymmetric unit" is that copies will
produce exactly the crystal lattice with no duplicate atoms. The "half
benzenes" having 4 atoms doesn't conform to this definition. It is not
important as you are not interested in joining the half benzenes.<br>
<br>
The unit cell dialog with the option to specify the number of cells
along each axis will be in tonight's builds.<br>
<br>
Tom<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] Problem with benzenes split across crystal
unit cell<br>
From: Michael Day <br>
To: 'Chimera BB' <br>
Date: 9/4/09 2:57 PM<br>
<blockquote cite="mid:D04E0D69-9ECD-4A5F-9555-A2CDCE3AAA2D@caltech.edu"
type="cite">Hi Tom,
<div><br>
</div>
<div>I've attached three screen shots corresponding to iat03.pdb,
solvent only, no solvent and everything. If solvent is the only thing
it gives different results than for the whole asymmetric unit.</div>
<div><br>
</div>
<div>I assume the change in unit cell will be in the next daily build?</div>
<div><br>
</div>
<div>The second problem is not really an issue because it helps force
the idea that these half molecules really are half molecules. I didn't
really expect Chimera to draw the bonds. The reason there are four
atoms is that two of them sit on the 2-fold (through 0,y,1/4 or
0,-y,3/4 or 1/2, 1/2+y, 1/4 or 1/2, 1/2-y, 3/4). If the benzene sat on
an inversion center then there would only be three of them.</div>
<div><img apple-width="yes" apple-height="yes"
src="cid:part1.08030302.00000200@cgl.ucsf.edu" height="240" width="307"><img
apple-width="yes" apple-height="yes"
src="cid:part2.03070701.00070109@cgl.ucsf.edu" height="240" width="271"><img
apple-width="yes" apple-height="yes"
src="cid:part3.08070400.03010601@cgl.ucsf.edu" height="240" width="265"> <br>
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<div>
<div>Cheers,</div>
<div>Mike</div>
<div><br>
</div>
<div><<<
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<div>Dr. Michael W. Day</div>
<div>Director - X-ray Crystallography Lab & Molecular Observatory</div>
<div>California Institute of Technology</div>
<div>Mail Code 139-74</div>
<div>Pasadena, CA 91125</div>
<div><br>
</div>
<div><<<
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<div>
<div>On Sep 4, 2009, at 1:42 PM, Tom Goddard wrote:</div>
<br class="Apple-interchange-newline">
<div bgcolor="#ffffff" text="#000000"> Hi Mike,<br>
<br>
The Chimera unit cell dialog is behaving as expected in the cases
where the asymmetric unit contains half of a benzene ring. First,
parts of the asymmetric unit are not moved relative to other parts of
the asymmetric unit, so as you observe the half benzenes in asymmetric
unit copies sometimes lie outside the unit cell. All unit cell dialog<br>
just puts the center of the asymmetric unit in the unit cell box. A
second problem is that a half benzene ring from one asymmetric unit
will not be joined to a half benzene ring from another asymmetric
unit. They will line up perfectly but Chimera does not see bonds
between the two halfs so for instance, selecting aromatic rings won't
pick those up.<br>
<br>
I guess the first problem could be handled by moving each connected
group of atoms so its center lies in the unit cell. I think it could
lead to undesired results. For example a protein with a bound ligand
might have the ligand outside the unit cell causing it to be moved to
some other asymmetric unit's binding site. The trouble with that is
that the protein and ligand are part of one molecule model in Chimera,
so now you have taken the ligand in that molecule and placed it with
the protein of another copy of the molecule. That may not be what you
want.<br>
<br>
Another answer to the first problem, is that I added to the unit cell
dialog the ability to make multiple asymmetric unit copies to fill
multiple unit cells. If you make several unit cells, then the half
benzenes lying outside one unit cell do join up with the half benzenes
from a different unit cell.<br>
<br>
If you were trying to make a figure and you didn't want half-benzenes
floating around -- you could simply select them and delete them
(Actions / Atoms / Delete).<br>
<br>
The second problem is harder. Chimera could guess that the
half-benzenes should be joined since they have exactly coincident
atoms. (This relies on the strange inconsistency that the
half-benzenes in the PDB files you sent contain 4 atoms instead of the
expected 3 atoms. So it doesn't actually represent an asymmetric unit
since there is an extra atom that will be duplicated in other
asymmetric units.) But Chimera can't join them because covalent bonds
can't be formed between different molecule objects -- it would require
making a new molecule to contain all the atoms. Creating extra
molecule models to join the half benzenes is possible but weird.<br>
<br>
Tom<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] Centro-symmetric space groups<br>
From: Michael Day <br>
To: Tom Goddard <br>
Date: 9/4/09 12:41 PM<br>
<blockquote
cite="mid:37EC1BEC-4B90-4EC0-BE51-4A862A2A10FA@caltech.edu" type="cite">Hi
Tom,
<div><br>
</div>
<div>Thanks. It looks like the issue is mostly resolved. </div>
<div><br>
</div>
<div>The is a problem with molecular units sitting at symmetry
element in non-primitive cells, for now I've found it in C2/c
(iat03.pdb) and Fdd2 (ta21.pdb) which I've attached. As far as I can
tell this is not unique to chimera, some programs handle this okay,
many don't. You'll see that in these two cases benzene molecules land
outside of the cell or fail to complete a pair.</div>
<div><br>
</div>
<div>If I had to lobby for any particular ticket on your list it
would be #201. What I would add in way of description on that ticket is
that I'm not talking about using SHELX in Chimera. What I meant to say
is for Chimera to read a standard format CIF file containing the
reciprocal space transform of the real space electron density. The fft
routines to transform back to real space have been around forever and
are in most all modern languages. </div>
<div><br>
</div>
<div>All crystallography packages can write this type of file
containing h,k,l F(obs)^2^, sig(F(obs)^2^), F(calc) and phi (phase
angle in degrees). This the preferred format for sending data to the
PDB.</div>
<div><br>
</div>
<div>I'm not looking to add a bunch of "stuff" to your already huge
pile but I thought most of this was already in the public domain. After
all, nothing is impossible for the guy that doesn't have to do it. It's
all easy and straightforward, right? ;0)</div>
<div><br>
</div>
<div>As for the issue of reading the CIF, P21/n is a very common
alternate setting of P21/c and the PDB symmetry list does not contain
it.</div>
<div><br>
</div>
<div>Thanks again!!<br>
<div apple-content-edited="true"> <span class="Apple-style-span"
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<div>
<div>
<div>Cheers,</div>
<div>Mike</div>
<div><br>
</div>
<div><<<
------------------------------------------------------------------------>>></div>
<div>Dr. Michael W. Day</div>
<div>Director - X-ray Crystallography Lab & Molecular
Observatory</div>
<div>California Institute of Technology</div>
<div>Mail Code 139-74</div>
<div>Pasadena, CA 91125</div>
<div><br>
</div>
<div><<<
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</div>
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</div>
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<div>
<div>On Sep 2, 2009, at 5:54 PM, Tom Goddard wrote:</div>
<br class="Apple-interchange-newline">
<div bgcolor="#ffffff" text="#000000"> Hi Mike,<br>
<br>
I've fixed the unit cell dialog to handle inverting symmetries. It
was a simple change. Will be in tonight's daily builds.<br>
<br>
We could have Unit Cell work with CIF files but that is an
enhancement that will have to compete for time with the hundreds of
other feature requests we're looking at. My list of requests is here<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests">http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests</a><br>
<br>
and Eric and other developer maintain their own off-line lists. So you
need to make a good case. It could be an easy task if our third-party
CIF file reader already parses the needed symmetry operators. If it
does not provide those then it could be a significant bit of work.<br>
<br>
Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] Centro-symmetric space groups<br>
From: Michael Day<br>
To: Thomas Goddard <br>
Date: 9/1/09 1:19 PM<br>
<blockquote
cite="mid:9AE9942C-32E2-48F5-A7D8-B5B90C38B3C5@caltech.edu" type="cite">Hi
Tom,
<div><br>
</div>
<div>Thanks.</div>
<div><br>
</div>
<div>Another option you might consider is to have the Unit Cell
tool work also with CIF files then only coordinate transformations are
needed as the symmetry operators are included. An advantage is that if
someone uses a non-standard setting of a space group the symmetry
operators are still valid for the coordinates.</div>
<div><br>
</div>
<div>Thanks for all your work. All of you on the Chimera team
(Elaine, Eric and Greg) set the bar pretty high! My hats off to you.</div>
<div><br>
<div apple-content-edited="true"> <span class="Apple-style-span"
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<div>
<div>
<div>
<div>
<div>
<div>
<div>Cheers,</div>
<div>Mike</div>
<div><br>
</div>
<div><<<
------------------------------------------------------------------------>>></div>
<div>Dr. Michael W. Day</div>
<div>Director - X-ray Crystallography Lab & Molecular
Observatory</div>
<div>California Institute of Technology</div>
<div>Mail Code 139-74</div>
<div>Pasadena, CA 91125</div>
<br>
<div><<<
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</div>
</div>
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<div>
<div>On Sep 1, 2009, at 9:27 AM, Thomas Goddard wrote:</div>
<br class="Apple-interchange-newline">
<div>Hi Mike,<br>
<br>
Thanks for the suggestions. The coordinate transformations are
routine. The trouble is that the Chimera Molecule C++ code takes the
transformation matrix and orthonormalizes it to a proper rotation. So
the inversion operator of "P -1" gets changed to inverting x and y axes
but not the z axis. The orthonormalization is supposed to just fix
tiny round-off transformation problems, like matrices read from a PDB
file that have only 5 digits of precision. Really we should be warning
if a transformation is very far from a proper rotation.<br>
<br>
I'll let you know when the problem is fixed in the daily builds.<br>
<br>
<span class="Apple-tab-span" style="white-space: pre;"> </span>Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] Centro-symmetric space groups<br>
From: Michael Day<br>
To: Thomas Goddard <br>
Date: 8/31/09 7:54 PM<br>
<br>
<blockquote type="cite">Tom,<br>
</blockquote>
<blockquote type="cite">Thanks again. Awesome!<br>
</blockquote>
<blockquote type="cite">I suspect mirrors and therefore glide
planes could be an issue as you don't see them in proteins.<br>
</blockquote>
<blockquote type="cite">I don't know what your overall strategy
is for applying space group operators but to avoid issues I would
suggest;<br>
</blockquote>
<blockquote type="cite">1) deorthogonalize into crystallographic
coordinates as fractions of cell edge<br>
</blockquote>
<blockquote type="cite">2) apply symmetry operators in turn to
the original set (x,y,z) to get (x',y',z') for each operator<br>
</blockquote>
<blockquote type="cite">3) calculate the centroid for each
equivalent set of coordinates (x',y',z')<br>
</blockquote>
<blockquote type="cite">4) move centroids into unit cell as
needed so they are x=0,1 y=0,1 and z=0,1<br>
</blockquote>
<blockquote type="cite">I suspect you already know this but it
never hurts to say it. My students think I overstate the basics at
times but it sure helps all of us get on the same page.<br>
</blockquote>
<blockquote type="cite">Cheers,<br>
</blockquote>
<blockquote type="cite">Mike<br>
</blockquote>
<blockquote type="cite"><<<
------------------------------------------------------------------------>>><br>
</blockquote>
<blockquote type="cite">Dr. Michael W. Day<br>
</blockquote>
<blockquote type="cite">Director - X-ray Crystallography Lab
& Molecular Observatory<br>
</blockquote>
<blockquote type="cite">California Institute of Technology<br>
</blockquote>
<blockquote type="cite">Mail Code 139-74<br>
</blockquote>
<blockquote type="cite">Pasadena, CA 91125<br>
</blockquote>
<blockquote type="cite">><br>
</blockquote>
<blockquote type="cite"><<<
------------------------------------------------------------------------>>><br>
</blockquote>
<blockquote type="cite">On 31 Aug, 2009, at 6:14 PM, Thomas
Goddard wrote:<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Hi Mike,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> Oops. The symmetries that invert
coordinates don't work in the Unit Cell tool. This is because it sets
the transformation matrix (rotation and shift) for the asymmetric unit
copies but it can only handle proper rotations. Chimera is generally
used for proteins which are handed (not symmetric under inversion) so
such space groups generally don't occur for proteins. But of course
for small molecules they can.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> I'll fix this soon, maybe later this
week. I'll have to change atom coordinates instead of setting the
transform matrix for the asymmetric unit copies.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Tom<br>
</blockquote>
</blockquote>
</div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
<br>
</div>
</div>
<br>
</div>
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