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Topics - cllawson

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RNA structures (DSSR) / DSSR eta-base theta-base
« on: January 09, 2021, 09:05:52 am »
Dear Xiangjun, 

Wishing you a Happy New Year! 

I have a request regarding DSSR json output for pseudotorsion angles.  I noticed that when backbone is present but no base has been modelled,  eta-base and theta-base values are listed as 0.0 and 0.0. Could you instead assign "null" as done for other pseudotorsion angles that cannot be calculated?  (e.g. eta for 1st residue in a polymer always shows as "null").  PDB ids where I noticed this issue: 6g4s (no bases deposited for entire structure), and 6sg9 (some residues with bases, others without).  Using: DSSR v1.9.10-2020apr23.



RNA structures (DSSR) / RNA Journal Covers
« on: July 28, 2020, 02:55:31 pm »
Ha just found this
Thank you Xiang-Jun for collating all of the 2019 journal covers I had created using X3DNA/blocview with pymol.
I have been testing out x3dna-dssr --cartoon-block today and it is much easier!
I will be using this great new option for all future NDB requests for covers.  :)

w3DNA -- web interface to 3DNA / w3dna server update schedule?
« on: August 08, 2019, 12:12:22 pm »
Hi Xiang-Jun,

I notice that ids for more recently released entries yield the following message from the w3DNA server: Empty or invalid ID, please type in a valid one.  (example:
So I'm wondering:
(1) how often the server is updated?
(2) since you can already analyze uploaded structures on the fly have you thought about enabling option to pull/analyze coordinates for newer PDB entries?

Thanks, Cathy

General discussions (Q&As) / x3dna-v2.3 no backbone ribbon
« on: July 31, 2018, 12:28:39 pm »
Hi Xiang-Jun,

I have been trying to replicate the images that appear on NDB using your latest x3dna package (v2.3) on Mac OS. 

When i run blocview filename.pdb, I get the message:

cannot find 'render'
no image output; 'blocview.r3d' -- to be fed into render/pymol

Which is fine because I have MacPymol so I can view/snap images of the r3d file. 

However, the images I get do not include the backbone ribbon, even though it seems it should be the default to include it (blocview --help states that --no-ds turns it off), so this seems like a bug.

I've attached an example image.

Thanks in advance for your help!

RNA structures (DSSR) / using DSSR ct files for input to VARNA
« on: May 24, 2016, 12:13:00 pm »
Dear Xiang-jun,

I have been looking at using VARNA for creating 2D maps of RNA, following what you showed us when we met a few weeks ago.
For the PDB entry 3RG5 (2 tRNA's in the asymmetric unit), VARNA is readily able to read/display using the .ct file DSSR creates for the whole entry from the cif file,
though the result is displeasing--two overlapped tRNAs.

Wwhen I tried to read in either of the individual chain .ct files VARNA chokes (e.g., java.lang.ArrayIndexOutOfBoundsException: -7). 
I've attached one of the problem ct files, wondering if you have seen this type of issue?

Feature requests / change eta-theta range?
« on: April 18, 2014, 03:25:09 pm »
Hi Xiang-Jun,

For your new program DSSR,  I notice that in the torsion output file the eta, theta, eta', and theta' ranges are -180 to +180, whereas the Pyle group's plots use the range 0 to 360.  With 0-360 for eta and theta (or eta' and theta'), the large helical peak falls nicely near the center, whereas with -180 to +180 the peak is split on the edges.  Could you either change to the default range for output of these pseudotorsions or add an option that allows listing in 0-360 range?

Many thanks,


RNA structures (DSSR) / DSSR release -- Congratulations!
« on: March 10, 2014, 05:34:39 pm »
Hi Xiang-Jun,
Just downloaded and did a quick test of DSSR today after receiving the notice about it from the "3DNA Forum Team".
Results look great!  Many thanks for creating this and making it available.
Cheers,  Cathy

General discussions (Q&As) / error bars in DNA parameters
« on: December 17, 2008, 11:11:27 am »
Dear Xiang-Jun,

 Can you advise the best way to determine or estimate error in parameters such as slide, twist, roll, x-displacement for a given estimated coordinate error?   (in our case refinement programs indicate the coordinate error is ~0.3 Angstroms).



My question is how to interpret 3DNA output for local base-pair helical parameters, since they are given in terms of a base-pair step, unlike the output of other programs.  I understand that the minimum local environment needed to define the local parameters is the base-pair step, but I am still a bit confused.

Local base-pair helical parameters
    step       X-disp    Y-disp   h-Rise     Incl.       Tip   h-Twist
   1 CG/CG     -1.27     -0.65      3.09     14.77      5.57     33.94

Are the values listed above defining parameters for the 1st base-pair relative to the 2nd, or the 2nd base-pair relative to the 1st, or is there a different explanation?


Cathy Lawson

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.