Re: [ccp4bb] Calculating over all bend in a DNA
Dear Sasha, you can select two pairs of three corresponding atoms at either end of the stand and calculate the plane normal of each set. The angle between the normals would be the overall bend. Best, Tim On 10/21/2014 09:53 PM, Sasha Pausch 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)? -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
[ccp4bb] Fwd: Re: [ccp4bb] Calculating over all bend in a DNA
Dear Sasha, dear all, I meant 'two _sets_ of three atoms each'. Thanks to Mark for pointing this out to me. Best, Tim Forwarded Message Subject: Re: [ccp4bb] Calculating over all bend in a DNA Date: Wed, 22 Oct 2014 10:50:10 +0200 From: Tim Gruene t...@shelx.uni-ac.gwdg.de Reply-To: Tim Gruene t...@shelx.uni-ac.gwdg.de To: CCP4BB@JISCMAIL.AC.UK Dear Sasha, you can select two pairs of three corresponding atoms at either end of the stand and calculate the plane normal of each set. The angle between the normals would be the overall bend. Best, Tim On 10/21/2014 09:53 PM, Sasha Pausch 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)? -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] Calculating over all bend in a DNA
Hi Sasha - you can use 3DNA: http://x3dna.org/; http://w3dna.rutgers.edu/ HTH, val On 21 October 2014 20:53, Sasha Pausch sashapau...@gmail.com 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)?
Re: [ccp4bb] Calculating over all bend in a DNA
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: blaine-moo...@ouhsc.edu 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 [CCP4BB@JISCMAIL.AC.UK] on behalf of Valerie Pye [val...@googlemail.com] Sent: Wednesday, October 22, 2014 6:10 AM To: CCP4BB@JISCMAIL.AC.UK 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%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=W0wpHNp%2B8HgFTfPnP6qooGcmzdq8AE7MNR43ZgeBMfQ%3D%0As=af3103f233522fb093353110ed7e13d1eed31bf25752556b48cba4b59d77da85; http://w3dna.rutgers.edu/https://urldefense.proofpoint.com/v1/url?u=http://w3dna.rutgers.edu/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=W0wpHNp%2B8HgFTfPnP6qooGcmzdq8AE7MNR43ZgeBMfQ%3D%0As=cbdb78f021cd77670fe306d17f761286b2f1c9550d9e296f664f0dac18f60b2e HTH, val On 21 October 2014 20:53, Sasha Pausch sashapau...@gmail.commailto:sashapau...@gmail.com 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)?
Re: [ccp4bb] Calculating over all bend in a DNA
Hello CCP4bb, Based on suggestions from the members of CCP4bb, I used program Curves+ to check the bend (angle) in DNA. I have given my DNA which has two strands and 13 bases each as an input. I got an output file where I can see other parameters inferred from the structure. But I am getting a message at the end of the output file which I believe gives me answer for my question. (E) Groove parameters No groove analysis: Pabsent in strand = 1 at level = 11 Please indicate to me what could be the error in this? Thank you all for answers, On Wed, Oct 22, 2014 at 2:20 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Sasha, you can select two pairs of three corresponding atoms at either end of the stand and calculate the plane normal of each set. The angle between the normals would be the overall bend. Best, Tim On 10/21/2014 09:53 PM, Sasha Pausch 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)? -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] Calculating over all bend in a DNA
Hello CCP4bb, May I know how can we calculate or use any server which can calculate the overall bend in a DNA (crystal structure)?
