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Topics Related to the 3DNA Software Package for the Analysis, Rebuilding & Visualization of Three-dimensional Nucleic Acid Structures
General discussions (Q&As)
Moderator: xiangjun
99 topics • Page 1 of 2 • 1, 2
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- Deformability of a small DNA fragment
by luhong » Mon Nov 23, 2009 9:05 pm - 2 Replies
- 4 Views
- Last post by luhong
Tue Nov 24, 2009 1:57 am
- Deformability of a small DNA fragment
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- From DNA sequence to DNA structure
by cif077 » Wed Nov 18, 2009 4:06 am
- 3 Replies
- 22 Views
- Last post by cif077
Fri Nov 20, 2009 1:24 am
- From DNA sequence to DNA structure
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- NUPARM vs X3DNA twist values
by kailsen » Mon Nov 09, 2009 11:11 pm
- 2 Replies
- 25 Views
- Last post by kailsen
Fri Nov 13, 2009 1:58 am
- NUPARM vs X3DNA twist values
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- About DNA contour length
by candery » Thu Oct 29, 2009 3:06 am - 1 Replies
- 15 Views
- Last post by xiangjun
Fri Oct 30, 2009 8:57 pm
- About DNA contour length
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- Who get 3DNA version 2.0
by 1982leoyao » Tue Sep 22, 2009 5:44 am - 1 Replies
- 34 Views
- Last post by ramon989
Thu Oct 22, 2009 3:35 am
- Who get 3DNA version 2.0
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- DNA rotation cont'd
by lrush88 » Sat Oct 17, 2009 1:16 pm - 1 Replies
- 21 Views
- Last post by xiangjun
Sat Oct 17, 2009 6:31 pm
- DNA rotation cont'd
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- 3DNA calculation for Bases that have two conformers in pdb
by kailsen » Thu Oct 08, 2009 12:29 am - 2 Replies
- 19 Views
- Last post by kailsen
Sat Oct 10, 2009 6:15 am
- 3DNA calculation for Bases that have two conformers in pdb
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- Option not to display calculation status to screen.
by esguerra » Wed Sep 02, 2009 12:33 pm - 2 Replies
- 20 Views
- Last post by esguerra
Thu Sep 03, 2009 3:52 pm
- Option not to display calculation status to screen.
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- trajectory analysis: error with analyze
by vmsrvignesh » Wed Aug 05, 2009 2:02 pm - 3 Replies
- 43 Views
- Last post by vmsrvignesh
Tue Aug 11, 2009 12:57 am
- trajectory analysis: error with analyze
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- defining a local helix axis
by mark » Wed Jul 08, 2009 1:23 pm - 2 Replies
- 52 Views
- Last post by mark
Thu Jul 09, 2009 2:32 pm
- defining a local helix axis
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- DNA Rotation
by lrush88 » Wed Jul 08, 2009 11:06 pm - 1 Replies
- 30 Views
- Last post by xiangjun
Wed Jul 08, 2009 11:50 pm
- DNA Rotation
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- Threading DNA
by Dilip » Mon Jun 22, 2009 1:20 pm - 1 Replies
- 37 Views
- Last post by xiangjun
Mon Jun 22, 2009 10:17 pm
- Threading DNA
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- How to make blocview -i work with pymol in batch mode.
by esguerra » Wed May 20, 2009 2:45 pm - 1 Replies
- 26 Views
- Last post by xiangjun
Wed May 20, 2009 7:03 pm
- How to make blocview -i work with pymol in batch mode.
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- Noobie question on building triplex DNA
by jporta » Thu Apr 30, 2009 12:37 pm - 2 Replies
- 53 Views
- Last post by jporta
Fri May 01, 2009 10:43 am
- Noobie question on building triplex DNA
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- how to minimize DNA built with fiber?
by pqtak » Wed Apr 22, 2009 8:41 pm - 4 Replies
- 27 Views
- Last post by pqtak
Mon Apr 27, 2009 4:10 pm
- how to minimize DNA built with fiber?
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- how the cartesian coordinates transform to PDB format
by yangsy » Mon Apr 20, 2009 4:02 am
- 5 Replies
- 86 Views
- Last post by ramon989
Wed Apr 22, 2009 11:35 am
- how the cartesian coordinates transform to PDB format
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- Find DNA-protien contacts using 3DNA
by ghzheng » Thu Apr 16, 2009 11:12 am - 1 Replies
- 70 Views
- Last post by xiangjun
Sat Apr 18, 2009 1:45 pm
- Find DNA-protien contacts using 3DNA
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- 3DNA has a web interface now
by ghzheng » Tue Apr 07, 2009 3:40 pm - 0 Replies
- 54 Views
- Last post by ghzheng
Tue Apr 07, 2009 3:40 pm
- 3DNA has a web interface now
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- Calculation of Jtwist, Jroll and Jslide for junctions
by venkadesh » Tue Mar 31, 2009 11:21 am - 3 Replies
- 32 Views
- Last post by xiangjun
Wed Apr 01, 2009 9:07 pm
- Calculation of Jtwist, Jroll and Jslide for junctions
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- SCHNArP/SCHNAaP c source code
by clarebonk » Wed Mar 11, 2009 7:59 pm - 6 Replies
- 97 Views
- Last post by clarebonk
Fri Mar 20, 2009 10:36 am
- SCHNArP/SCHNAaP c source code
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- Building a DNA superhelix
by molatwork » Tue Mar 03, 2009 10:58 am - 3 Replies
- 87 Views
- Last post by xiangjun
Thu Mar 05, 2009 12:16 am
- Building a DNA superhelix
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- Base Pair Step Parameters
by rodrigopontiggia » Mon Feb 16, 2009 3:41 pm
- 3 Replies
- 204 Views
- Last post by xiangjun
Sat Feb 21, 2009 2:05 pm
- Base Pair Step Parameters
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- stability of rna structure
by balasubramanian » Mon Feb 09, 2009 6:41 am
- 1 Replies
- 119 Views
- Last post by xiangjun
Wed Feb 11, 2009 9:39 pm
- stability of rna structure
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- unknown step values
by yangxi » Wed Feb 04, 2009 11:04 pm - 2 Replies
- 87 Views
- Last post by yangxi
Thu Feb 05, 2009 11:10 pm
- unknown step values
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- error bars in DNA parameters
by cllawson » Wed Dec 17, 2008 12:11 pm - 1 Replies
- 221 Views
- Last post by xiangjun
Wed Dec 17, 2008 10:56 pm
- error bars in DNA parameters
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- Continuous polymer
by ovelha » Tue Dec 02, 2008 2:11 pm - 2 Replies
- 195 Views
- Last post by ghzheng
Tue Dec 09, 2008 2:00 pm
- Continuous polymer
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- 3DNA misses one pair of nucleotides
by pqtak » Tue Oct 28, 2008 1:16 pm - 3 Replies
- 282 Views
- Last post by pqtak
Sun Nov 02, 2008 11:55 pm
- 3DNA misses one pair of nucleotides
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- sugar puckers in B-DNA
by pqtak » Sat Oct 25, 2008 1:09 am - 0 Replies
- 154 Views
- Last post by pqtak
Sat Oct 25, 2008 1:09 am
- sugar puckers in B-DNA
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- ideal values for the stacking parameters
by Miguel » Tue Oct 07, 2008 4:12 pm - 1 Replies
- 252 Views
- Last post by xiangjun
Fri Oct 10, 2008 11:03 pm
- ideal values for the stacking parameters
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- Calculating the angle of DNA curvature
by wkagawa » Thu Sep 25, 2008 2:02 am - 2 Replies
- 525 Views
- Last post by wkagawa
Fri Oct 03, 2008 12:44 am
- Calculating the angle of DNA curvature
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- local helical parameters interpretation question
by cllawson » Tue Sep 16, 2008 6:17 pm - 3 Replies
- 438 Views
- Last post by xiangjun
Thu Sep 18, 2008 12:02 am
- local helical parameters interpretation question
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- interhelical angles
by btolbert » Mon Sep 15, 2008 5:33 pm - 1 Replies
- 206 Views
- Last post by xiangjun
Tue Sep 16, 2008 9:13 pm
- interhelical angles
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- Unknown residue DC
by alokjain » Sat Sep 13, 2008 1:19 am - 1 Replies
- 249 Views
- Last post by ghzheng
Tue Sep 16, 2008 4:32 pm
- Unknown residue DC
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- interpretation of output file
by pqtak » Sat Aug 09, 2008 12:18 pm - 8 Replies
- 540 Views
- Last post by pqtak
Sat Sep 13, 2008 7:42 pm
- interpretation of output file
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- Rebuilding protonated RNAs with non-canonical basepairs
by ramon989 » Wed Jul 23, 2008 7:50 am
- 4 Replies
- 331 Views
- Last post by ramon989
Thu Jul 31, 2008 12:23 pm
- Rebuilding protonated RNAs with non-canonical basepairs
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- calculate step parameters of a funny step
by feix » Wed Jul 23, 2008 10:54 am
- 2 Replies
- 324 Views
- Last post by feix
Thu Jul 24, 2008 12:35 pm
- calculate step parameters of a funny step
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- Multiple global helical axes in one structure, how to calc?
by ramon989 » Wed Jun 25, 2008 3:51 am - 1 Replies
- 339 Views
- Last post by xiangjun
Wed Jun 25, 2008 9:55 pm
- Multiple global helical axes in one structure, how to calc?
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- rotate_mol rotfile.dat
by Marcp » Tue Jun 10, 2008 5:13 am - 2 Replies
- 341 Views
- Last post by Marcp
Fri Jun 13, 2008 4:12 am
- rotate_mol rotfile.dat
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- Dealing with DNA-Protein complexes
by Marcp » Mon Apr 28, 2008 1:06 pm
- 6 Replies
- 718 Views
- Last post by Marcp
Tue May 13, 2008 3:34 am
- Dealing with DNA-Protein complexes
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- Small bug in find_pair
by Liron Bar » Sun Apr 13, 2008 7:41 pm - 1 Replies
- 453 Views
- Last post by xiangjun
Mon Apr 14, 2008 10:31 pm
- Small bug in find_pair
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- Baselist.dat
by Auffinger » Tue Apr 08, 2008 11:45 am
- 2 Replies
- 356 Views
- Last post by Auffinger
Thu Apr 10, 2008 12:16 pm
- Baselist.dat
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- 3DNA on Red Hat Linux WS v5
by Wimal Pathmasiri » Mon Mar 24, 2008 11:23 am - 1 Replies
- 523 Views
- Last post by xiangjun
Mon Mar 24, 2008 10:06 pm
- 3DNA on Red Hat Linux WS v5
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- SwS : Solvation web Service for nucleic acids
by Auffinger » Mon Mar 17, 2008 10:53 am - 1 Replies
- 496 Views
- Last post by xiangjun
Mon Mar 17, 2008 11:04 pm
- SwS : Solvation web Service for nucleic acids
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- Global linear helical axis calculation in 3DNA
by kateryna » Wed Mar 12, 2008 12:08 pm - 3 Replies
- 466 Views
- Last post by xiangjun
Thu Mar 13, 2008 8:02 pm
- Global linear helical axis calculation in 3DNA
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- problems with stacking parameters of a MD-history
by Miguel » Thu Mar 06, 2008 2:26 pm - 3 Replies
- 370 Views
- Last post by xiangjun
Fri Mar 07, 2008 8:26 pm
- problems with stacking parameters of a MD-history
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- 3DNA ppc64 GNU/linux architecture
by raist » Mon Feb 25, 2008 3:46 am - 2 Replies
- 450 Views
- Last post by raist
Fri Mar 07, 2008 5:32 am
- 3DNA ppc64 GNU/linux architecture
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- helical Parameters of a Modified nucleic acids
by Mathew » Sat Feb 02, 2008 1:18 pm
- 8 Replies
- 523 Views
- Last post by Mathew
Thu Feb 21, 2008 11:04 pm
- helical Parameters of a Modified nucleic acids
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- I uploaded a 3DNA parser
by yrxin » Thu Jan 17, 2008 10:33 pm - 0 Replies
- 408 Views
- Last post by yrxin
Thu Jan 17, 2008 10:33 pm
- I uploaded a 3DNA parser
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- parameters to define quasi-continuous helix
by yrxin » Fri Nov 16, 2007 12:27 pm - 1 Replies
- 645 Views
- Last post by xiangjun
Sat Nov 17, 2007 8:53 pm
- parameters to define quasi-continuous helix
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- Non-canonical base pairing
by Guest » Tue Oct 30, 2007 10:58 am
- 3 Replies
- 830 Views
- Last post by xiangjun
Fri Nov 02, 2007 1:10 am
- Non-canonical base pairing
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