[phenixbb] Cell dimentions

Terwilliger, Thomas Charles terwilliger at lanl.gov
Sat Aug 29 15:00:53 PDT 2015

Hi Bradley,

I'd say what you want to do depends on the actual situation in the crystal. Here are two possibilities, the first one is I think what you are describing:

A. The asymmetric unit of the crystal contains two chains that are in different conformations. The asymmetric unit is twice as large as you had originally guessed.

B. There are two conformations present in the crystal for each chain, but the conformers are in effect random among all the chains.  This situation could best be described as having multiple conformations in the asymmetric unit, with 1 chain as the asymmetric unit.

For situation A, there will be twice as many unique reflections to be measured. Either:

(1) the cell will be doubled, in which case there will be many reflections with near-zero intensity but there must be some with non-zero intensity as these are the ones that define what is different between the two otherwise-equivalent chains.

or (2) some element of symmetry in the crystal will be missing.  In this situation there will be reflections that are no longer equal in intensity though they would have been by crystal symmetry.

I would say unless you can demonstrate (1) or (2) above it is probably not a good idea to say that situation A exists.

For case B, the crystal symmetry is what you original thought it to be; there are just multiple conformations and these can be dealt with in the usual way with conformer A and B labels.

Let me know if that doesn't help,
All the best,
Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Bradley Hintze [bradley at hintze.org]
Sent: Saturday, August 29, 2015 3:18 PM
To: PHENIX user mailing list
Subject: [phenixbb] Cell dimentions


I have some interesting DNA structures I would like help with . The duplexes are stacked in the crystal head to head and tail to tail. This creates an interesting situation where an adenine is base pairing with itself across cell symmetry. The most likely way in which adenines base pairs with itself is if one is in the syn conformation and the other is in anti, i.e. a Hoogsteen base pair. However, that would break the symmetry as they are the same adenine and thus can't have two conformations. As such, I think it's appropriate to have two molecules, rather than one, in the asymmetric unit. I can make the new model easily enough by generating a symmetry mate and assigning different chain IDs but how do I appropriately calculate the new cell dimensions?


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