Hi Sasha, You can also use Richard Lavery's webservice for Curves+ ( http://gbio-pbil.ibcp.fr/cgi/Curves_plus/ ) and visualize the curve of the helical axis in 3D in a molecular graphics program.
In addition, you can do a normal vector analysis similar to the one suggested by Tim Gruene by running FREEHELIX by Richard Dickerson which has been available through the fink depository and which could be found this morning at the Nucleic Acid Databank via http://ndbserver.rutgers.edu/files/ftp/NDB/programs/freehelix98. Linux binaries and the source code are available. I was able to compile from source code on a Mac several years ago. Examples of our use of these programs as applied to two RNAs are found in PMID: 21878548. Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Shipping address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Letter address: P.O. Box 26901, BRC 466 Oklahoma City, OK 73190 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: [email protected] Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d- Small Angle Scattering webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0 X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory ________________________________ From: CCP4 bulletin board [[email protected]] on behalf of Valerie Pye [[email protected]] Sent: Wednesday, October 22, 2014 6:10 AM To: [email protected] Subject: Re: [ccp4bb] Calculating over all bend in a DNA Hi Sasha - you can use 3DNA: http://x3dna.org/<https://urldefense.proofpoint.com/v1/url?u=http://x3dna.org/&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=W0wpHNp%2B8HgFTfPnP6qooGcmzdq8AE7MNR43ZgeBMfQ%3D%0A&s=af3103f233522fb093353110ed7e13d1eed31bf25752556b48cba4b59d77da85>; http://w3dna.rutgers.edu/<https://urldefense.proofpoint.com/v1/url?u=http://w3dna.rutgers.edu/&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=W0wpHNp%2B8HgFTfPnP6qooGcmzdq8AE7MNR43ZgeBMfQ%3D%0A&s=cbdb78f021cd77670fe306d17f761286b2f1c9550d9e296f664f0dac18f60b2e> HTH, val On 21 October 2014 20:53, Sasha Pausch <[email protected]<mailto:[email protected]>> wrote: Hello CCP4bb, May I know how can we calculate or use any server which can calculate the overall bend in a DNA (crystal structure)?
