Topics

1

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.

Thanks,

Cathy

2

RNA structures (DSSR) / RNA Journal Covers

« on: July 28, 2020, 02:55:31 pm »

Ha just found this http://docs.x3dna.org/images/3dna-RNA-covers.png
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. 

3

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: http://www.rcsb.org/structure/6I84).
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

4

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!

5

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?

6

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,

Cathy

7

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

8

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).

thanks,

Cathy

9

General discussions (Q&As) / local helical parameters interpretation question

« on: September 16, 2008, 06:17:49 pm »

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?

thanks,

Cathy Lawson