<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Smith,<div class=""><br class=""></div><div class=""> The Unit Cell tool shows 6 copies of the 2ZAM asymmetric unit. Since the crystal symmetry extends to infinity Chimera has to decide which 6 to show. How does it decide? There is nothing smart about it — it simply takes the 6 space group symmetry operators. Here they are for space group P65 taken from the 2ZAM.pdb header</div><div class=""><br class=""></div><div class=""><div class="">REMARK 290 CRYSTALLOGRAPHIC SYMMETRY </div><div class="">REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 </div><div class="">REMARK 290 </div><div class="">REMARK 290 SYMOP SYMMETRY </div><div class="">REMARK 290 NNNMMM OPERATOR </div><div class="">REMARK 290 1555 X,Y,Z </div><div class="">REMARK 290 2555 -Y,X-Y,Z+2/3 </div><div class="">REMARK 290 3555 -X+Y,-X,Z+1/3 </div><div class="">REMARK 290 4555 -X,-Y,Z+1/2 </div><div class="">REMARK 290 5555 Y,-X+Y,Z+1/6 </div><div class="">REMARK 290 6555 X-Y,X,Z+5/6 </div><div class="">REMARK 290 </div><div class="">REMARK 290 WHERE NNN -> OPERATOR NUMBER </div><div class="">REMARK 290 MMM -> TRANSLATION VECTOR </div><div class=""><br class=""></div><div class="">It applies those 6 translations and reflections (they are shown above in coordinates where unit cell size is 1,1,1). When you apply those 6 it doesn’t necessarily give you the closest packed 6 copies of your molecule. That is where the “pack” option in the Unit Cell dialog comes in. With “pack” enabled, after using those symmetry operators Chimera will shift each copy by one or more unit cells along each of the 3 axes so that the molecule center lies in the unit cell outline box that is displayed. If in the coordinates with unit cell size 1,1,1, the center of a molecule copy lies outside 0-1,0-1,0-1 then it shifts the coordinates by an integer along each axis so it lies inside. Such shifts just show the copy in the adjoining unit cell. You might want other choices of which 6 copies to show. To achieve that you could show 2 by 2 by 2 unit cells (48 = 6*2*2*2 copies) then simply delete the copies you don’t want.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div><blockquote type="cite" class=""><div class="">On Jan 31, 2017, at 10:19 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><br class=""></div><div class="">Hi Smith,</div><div class="">The Unit Cell results for a structure with and without “pack” are equivalent because the symmetry describes a repeating pattern: each single copy could be shown in any of several places around the first copy. In other words, as I said before, there are multiple equally correct ways of presenting the same information. </div><div class=""><br class=""></div><div class="">Although I cannot spend a lot of time looking at your specific data, I see the 3 structures are all the same space group with similar unit cell dimensions and angles, and the paper says “we could present nucleotide-induced conformational changes in the same crystal lattice by eliminating possible artificial structural differences because of different crystal packing.” Therefore I infer that the crystal packing is approximately the same in the 3 structures. It cannot be EXACTLY the same, however, since there are conformational changes between the structures.</div><div class=""><br class=""></div><div class="">Since I didn’t write the Unit Cell code or look at the symmetry matrices in detail, I don’t know why the structures don’t give the same arrangement without “pack,” but I don’t think it is important, since the different possible arrangements for a single structure are equally correct. I hope this helps,</div><div class="">Elaine</div><div class=""><div class="">
<span class="Apple-style-span" style="border-collapse: separate; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; border-spacing: 0px;"><div class=""><div class=""><br class=""></div></div><div class="">P.S. please send questions to chimera-users rather than to me individually - thanks</div></span>
</div>
<div class=""><br class=""><blockquote type="cite" class=""><div class="">Begin forwarded message:</div><br class="Apple-interchange-newline"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">"Smith Liu" <<a href="mailto:smith_liu123@163.com" class="">smith_liu123@163.com</a>><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Fw:Re: [Chimera-users] on chimera unit cell function</b><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">January 31, 2017 at 7:01:54 AM PST<br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><b class="">To: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a><br class=""></span></div><br class=""><div class=""><div style="line-height: 1.7; font-size: 14px; font-family: Arial;" class=""><div class=""><div class="">Dear Elaine,</div><div class=""><br class=""></div><div class="">Related to our previous communication on "on chimera unit cell function" , here I have more to discuss with you.</div><div class=""><br class=""></div><div class="">Attached 1 was the paper “Nucleotide-Dependent Conformational Changes and</div><div class="">Assembly of the AAA ATPase SKD1/VPS4B” published in Traffic 2008. PDB ID 2ZAM, 2ZAN, 2ZAO were 3 pdbs from this paper, and 2ZAM was the VPS4B without any nucleotide, 2ZAN was the VPS4B bound with ATP, 2ZAO as the VPS4B bound with ADP.</div><div class=""> </div><div class="">As the paper wrote, “Because our attempts to crystallize SKD1 (VPS4B) in the presence</div><div class="">of ATP or ADP failed, we soaked the apo form crystals in solutions of ATP or ADP”, thus the 2ZAN and 2ZAO were got by soaking the crystal for 2ZAM with ATP and ADP separately. All 3 crystals were with space group P 65.</div><div class=""> </div><div class="">The pdb for the 6 mates for each of 2ZAM, 2ZAN and 2ZAO are attached in attachment 2, 3, 4 separately (prepared without clicking ""Pack molecules in unit cell"). If viewed by Chimera, you will find the mates of 2ZAM arrange in the same way as the mates of 2ZAO, i.e., the 6 mates connect each other closely (side by side) and packed in a screw way. However for the 6 mates of 2ZAN, although still in screw way, the 6 mates arrange not closely but have a space between the adjacent mates. Correspondingly, the diameters of the z-axis projection of the 6 mates of 2ZAM and 2ZAO were much smaller than that of the 6 mates of 2ZAN.</div><div class=""><br class=""></div><div class="">However, if we by Chimera we click the "Pack molecules in unit cell",we will find the 6 mates of 2ZAN displayed exactly (or very similarly) as the 6 mates of 2ZAM and 2ZAO (Am I right).</div><div class=""><br class=""></div><div class="">Then my question would be, in the crystal for 2ZAN and 2ZAO, do the proteins arranged in exactly the same pattern? And why if we did not click ""Pack molecules in unit cell", the mates of 2ZAN and 2ZAO were displayed differently, and with clicking ""Pack molecules in unit cell",the mates of 2ZAN and 2ZAO were displayed similarly?</div><div class=""><br class=""></div><div class="">If the protein arranged differently in the crystal for 2ZAN and 2ZAO, then in the crystal packing of 2ZAN, how can I identify the 6 protein which were from the 6 screwed mates in 2ZAM?</div><div class=""><br class=""></div><div class="">I am looking forward to getting a reply from you.</div><div class="">Smith</div></div><pre class="">-------- Forwarding messages --------
From: "Elaine Meng" <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>>
Date: 2017-01-30 04:05:22
To: "Smith Liu" <<a href="mailto:smith_liu123@163.com" class="">smith_liu123@163.com</a>>
Cc: "<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>>
Subject: Re: [Chimera-users] on chimera unit cell function
Hi Smith,
The number of copies and their positions are all correct no matter whether you choose the “pack” option or not. If you cut out a part of the real crystal, there will be a real copy in the same place as the copy from Chimera. So imagine if you had specified an infinite (or large) number of unit cells in Chimera, a chunk from the middle of the result would look the same as some chunk of the real idealized crystal, regardless of whether you used “pack”. However, since you are probably specifying 1 x 1 x 1 or some small number of unit cells, yes choose the “pack” option to show the copies packed together, instead of with some spaces where a copy is shown inside a neighboring box rather than in the central outline box.
Best,
Elaine
> On Jan 29, 2017, at 5:10 AM, Smith Liu <<a href="mailto:smith_liu123@163.com" class="">smith_liu123@163.com</a>> wrote:
>
> Dear Elaine,
>
> I am still confusing on the function of "Pack molecules in unit cell" in Chimera. If we cut out a cube (or a volume) of crystal based on which a pdb was got, do you think the molecules packed in the cube in the way without "Pack molecules in unit cell" clicked, or the molecules packed in the cube in the way with "Pack molecules in unit cell" clicked?
>
> I am looking forward to getting a reply from you.
>
> Smith
>
>
> At 2017-01-29 00:50:44, "Elaine Meng" <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:
> >Hi Smith,
> >It is my understanding that you will get the same number of copies whether or not you choose the “pack” option, and that there are multiple equally correct ways in which the copies will be positioned according to the symmetry information. The “pack” option simply chooses, out of these many equally correct alternatives, a configuration that places the centers of all the copies inside one unit cell outline box instead of spreading them out among neighboring boxes.
> >I hope this helps,
> >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 28, 2017, at 1:47 AM, Smith Liu <<a href="mailto:smith_liu123@163.com" class="">smith_liu123@163.com</a>> wrote:
> >>
> >> Dear All,
> >>
> >> In Chimera, we do Tools →Higher-Order Structure→Unit Cell, then what will be the diffenrence if we clicked "Pack molecules in unit cell" in comparison with if we did not click "Pack molecules in unit cell"? Does it mean that what we observed (or what Chimera displayed) if we click "Pack molecules in unit cell" , was really part of what it displayed if we did not click "Pack molecules in unit cell" but we increased the "Number of Cells" significantly?
> >>
> >> I am looking forward to getting a reply from you.
> >>
> >> Smith
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