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It isn't clear to me what you mean by "not big enough" but there are indeed several other stacked-X junction structures beyond the two previously mentioned (over a dozen to my knowledge, most of which are published). The size of the central cavity is one feature that varies between these structures. Thus, 1) please clarify what you are attempting to accomplish and 2) check out other structures besides 1DCW. Refer to the supplemental material from Proc. Natl. Acad. Sci. USA. 2005 May 17;102(20):7157-62 for a survey of a few published junctions. There are several simple methods to apply translation and rotation matrices to one or both of the duplex junction arms if you want to increase the central cavity size. Four-fold and two-fold symmetric open-X junctions bound to protein are also available. More detail would be helpful. Frank -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jie Li, PhD Sent: Wednesday, November 23, 2005 2:15 PM To: [email protected] Subject: Re: [ccp4bb]: building a DNA four-way junction *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Firstly, thanks a lot to everyone who concerns. The problem is, for example, when I tried a 4-way junction model like 1DCW.pdb, I found the space in the middle of junction is not big enough. If I move DNA strands manually, it will make the conformation unreasonable. I dont know how to deal with such things. Thanks again. This e-mail message may contain information that is confidential and/or privileged. If you are not the intended recipient, any use, disclosure, copying, or communication of the contents of this message is prohibited. If this message was received in error, please delete the message and any attachments from your computer. Thank you.
