Recent Posts

51

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« Last post by Di_Liu on June 01, 2025, 09:08:25 pm »

Hi Xiang-Jun,

I checked your model, and I can confirm that it is what I wanted.

I'm also attaching the model I've built. The screenshot is a comparison of yours (blue) and mine (pink). I think we were using the G84 ring I've created, so our models can be overlayed. An extra step required for your model is to link the dinucleotide steps.

By the way, I think I figured out why I didn't get the email notification. I indeed received a notification on April 30, but I thought (mistakenly, probably due to the early morning...) I had already viewed the reply because you posted a reply on April 29, which was assumed to be the same message, so I didn't open a link for your April 30 message. I saw in the email that "More replies may be posted, but you won't receive any more notifications until you read the topic." I believe this setting is the reason I didn't the email notification of your follow-up message on May 5.

Best,

Di

52

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« Last post by Di_Liu on June 01, 2025, 08:39:40 pm »

Hi Xiang-Jun,

Thanks a lot for your following-up of my questions!

I'm sorry that I didn't look back into this question. And I don't know why I didn't receive an email notification about your reply. I remember that I always received an email notification whenever there was a reply to my message in the past...

I logged in today because I also have made progress to create the Z-DNA ring during the weekend, and wanted to let you know. Do you want me to post the details of my procedure?

Thanks again for your work, and I will check your model and let you know my opinion!

Best,

Di

53

RNA structures (DSSR) / Re: License requested

« Last post by xiangjun on May 31, 2025, 11:40:43 am »

Hi,

Thanks for your interest in DSSR, and for posting on this forum. I am aware of the issue, and put the following note in the Download instructions.

DSSR v1.9.10-2020apr23 --- This version corresponds to the paper "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" (2020) in Nucleic Acids Research. From version 2.0 (released around the summer of 2020), DSSR has been licensed by the Columbia Technology Ventures (CTV), who manages the free DSSR Academic licenses as well as paid DSSR Pro licenses for both academic and commercial users. I've lately learned of academic users from certain countries having trouble in getting DSSR Academic licenses. This pre-licensed version is provided (as is) here to fill the gap: it is slightly outdated but still works well. Whenever possible, however, users should obtain the latest version of DSSR through CTV --- it is free for academic uses and fully supported by the NIH R24GM153869 grant.

Best regards,

Xiang-Jun

54

RNA structures (DSSR) / License requested

« Last post by moloch on May 31, 2025, 08:56:06 am »

I have requested the License, may I ask when it will be approved?

55

MD simulations / Re: Base pair number not staying constant in simulations

« Last post by rkumar on May 30, 2025, 01:09:55 pm »

Hi,

Apologies for the late reply. Please use  -ref option to keep the base-pairs constant. However, any parameters calculated for broken base-pairs will be of extreme values. If base-pairs are broken at the terminals, then those could be ignored during analysis by dnaMD.

Thanks,
Rajendra

56

MD simulations / Re: Base pair number not staying constant in simulations

« Last post by xiangjun on May 21, 2025, 10:03:01 am »

Thanks for the detailed report. While @rkumar should be the primary contact for dnaMD related issues, I'd like to address the general question of why the base pair number not staying constant in simulations.

In 3DNA, the find_pair program is used to identify base pairs in an input structure. For MD trajectories, when each frame is processed with auto-detected base pairs, the numbers can fluctuate due to the dynamic nature of the system. The 3DNA suite includes the Ruby script x3dna_ensemble, and the beginning portion of the "x3dna_ensemble analyze -h" command is as follows. Basically, it requires a template base-pair input file, possibly generated with ‘find_pair’ and manually edited as necessary.

------------------------------------------------------------------------
Analyze a MODEL/ENDMDL delineated ensemble of NMR structures or MD
trajectories. All models must correspond to different conformations
of the same molecule. For the analysis of duplexes (default), a template
base-pair input file, generated with 'find_pair' and manually edited
as necessary, must be provided.

Usage:
        x3dna_ensemble analyze options
Examples:
        x3dna_ensemble analyze -b bpfile.dat -e sample_md0.pdb

In DSSR, the --nmr (or --md) option can be used with --pair-list-input to analyze MD trajectories with a customized set of base pairs of interest. See the DSSR User Manual for more details in Sections "3.13 The --nmr option" and "3.9 The --pair-list options".

Best regards,

Xiang-Jun

57

MD simulations / Base pair number not staying constant in simulations

« Last post by piia600 on May 21, 2025, 08:16:27 am »

Hi all,

I have managed to briefly analyze my simulations with dnaMD Python module. I managed to analyze the curvature of the unbound DNA but I ran into issues while analyzing the bound DNA.

The 3DNA calculations finish fine, but they identify different number of base pairs in different frames. There are 40 base pairs in the starting structure, but in some frames this drops to 35.

I can load the helical axis with step range defined:

complexdna.set_helical_axis('complex2/HelAxis_complex2_test.dat',step_range=True, step=[10,25])

But I can't continue the curvature analysis, because the command

complexdna.generate_smooth_axis(step_range=True, step=[10,25], smooth=500, spline=2, fill_point=6, cut_off_angle=180)

Leads to an error (which happens around the time when the base pair number goes very low):

Fitting spline curve on helical axis of frame 6000 out of 80000 frames
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[24], line 2
      1 # Generate global axis by interpolation (smoothening)
----> 2 complexdna.generate_smooth_axis(step_range=True, step=[10,25], smooth=500, spline=2, fill_point=6, cut_off_angle=180)
      4 # Calculate curvature and tangent along global helical axis
      5 #freedna.calculate_curvature_tangent(store_tangent=True)

File ~/.local/lib/python3.9/site-packages/dnaMD/dnaMD.py:1322, in DNA.generate_smooth_axis(self, step_range, step, smooth, spline, fill_point, cut_off_angle)
   1318     sys.stdout.write("\rFitting spline curve on helical axis of frame %d out of %d frames" % (
   1319         frame_number, nframes))
   1320     sys.stdout.flush()
-> 1322 xsmooth, ysmooth, zsmooth, mask = fit_axis(bp_idx, frame_number, RawX, RawY, RawZ, smooth, spline, fill_point, cut_off_angle)
   1323 maskArray = mask
   1325 smoothX.append(xsmooth)

File ~/.local/lib/python3.9/site-packages/dnaMD/dnaMD.py:2621, in fit_axis(bp_idx, nframe, RawX, RawY, RawZ, smooth, spline, fill_point, cut_off_angle)
   2618 points = fill_point * len(orig_x)
   2620 nest = -1
-> 2621 tckp, u = splprep([orig_x, orig_y, orig_z], s=smooth, k=spline, nest=nest)
   2623 xnew, ynew, znew = splev(np.linspace(0, 1, points), tckp)
   2625 new_axis = np.array([xnew, ynew, znew]).T

File /usr/local/lib/python3.9/site-packages/scipy/interpolate/_fitpack_py.py:155, in splprep(x, w, u, ub, ue, k, task, s, t, full_output, nest, per, quiet)
     13 def splprep(x, w=None, u=None, ub=None, ue=None, k=3, task=0, s=None, t=None,
     14             full_output=0, nest=None, per=0, quiet=1):
     15     """
     16     Find the B-spline representation of an N-D curve.
     17
   (...)
    152
    153     """
--> 155     res = _impl.splprep(x, w, u, ub, ue, k, task, s, t, full_output, nest, per,
    156                         quiet)
    157     return res

File /usr/local/lib/python3.9/site-packages/scipy/interpolate/_fitpack_impl.py:175, in splprep(x, w, u, ub, ue, k, task, s, t, full_output, nest, per, quiet)
    173 wrk = _parcur_cache['wrk']
    174 iwrk = _parcur_cache['iwrk']
--> 175 t, c, o = _fitpack._parcur(ravel(transpose(x)), w, u, ub, ue, k,
    176                            task, ipar, s, t, nest, wrk, iwrk, per)
    177 _parcur_cache['u'] = o['u']
    178 _parcur_cache['ub'] = o['ub']

ValueError: Invalid inputs.

Also the 3DNA HelAxis*.dat files contained ---- for some base pairs which were not understood by dnaMD. I needed to replace them with 0.00 to get the file read.

Could you help me get the curvature analyzed also for the bound DNA? I only used the DNA atoms in the analyzed bound trajectory to get a comparison with the unbound DNA.

If needed, I can share some files for testing.

58

MD simulations / Re: Do I need gromacs to use dnaMD for simulations?

« Last post by piia600 on May 20, 2025, 03:20:40 am »

Thanks for the help!

Now I have managed to install both 3DNA and do_x3DNA for GROMACS. However, it seems do_x3DNA needs 'residuetypes.dat' file form GROMACS installation. It seems I was able to bypass this by downloading the file form github and putting it in the working folder. I thought you might want to put a note of this to the documentation.

Keep up the good work!

59

MD simulations / Re: Do I need gromacs to use dnaMD for simulations?

« Last post by rkumar on May 19, 2025, 12:31:02 am »

Do I need GROMACS version of dnaMD to analyze simulations or can I use the Python module of dnaMD without GROMACS for simulations?

No, dnaMD is a python package purely written in python. However, it requires output from do_x3dna,  which is now available for direct download and does not require GROMACS installation. You can use both do_x3dna and dnaMD without requiring GROMACS installation.

Thanks,

60

MD simulations / Re: Do I need gromacs to use dnaMD for simulations?

« Last post by xiangjun on May 16, 2025, 10:00:09 am »

Thanks for the x3DNA-DSSR software which works wonderfully for single PDBs.

Thanks for using DSSR and for posting your questions on the 3DNA Forum. As for the analysis of an ensemble, please see the DSSR manual , especially Section: "3.13 The --nmr option":

The DSSR --nmr (or --md) option automates the analysis of an ensemble, such as NMR structures in the PDB or snapshots from MD simulations. The input coordinates file must be in either the classic PDB format where each model is delineated by MODEL/ENDMDL tags, or the mmCIF format where each ATOM/HETATM record has an associated model number.
...
The --json option makes it easy to parse the output of multiple models pragmatically. In addition to NMR structures, trajectories from MD simulations can also be processed. Popular MD packages (AMBER, GROMACS, CHARMM, etc.) all have their own specialized binary formats for trajectories. By design, DSSR does not work on these binary files. They must be converted to the standard PDB or mmCIF format to be analyzed by DSSR. The combination of --nmr and --json makes DSSR directly accessible to the MD community.

I have some MD simulations I would like to analyze with dnaMD. I ran them with Amber but converted them to GROMACS .xtc + .pdb files for analysis.

Do I need GROMACS version of dnaMD to analyze simulations or can I use the Python module of dnaMD without GROMACS for simulations?

I am not a practitioner of MD simulations. Questions related to dnaMD are best answered by its developer: hopefully @rkumar will chime in. See the thread Update of do_x3dna package, which can be used with files generated by GROMACS.

PS. I am also lacking the link to download the 3DNA from the forum for some reason, my forum view is similar to unregistered users.

There have been too many spam registrations nowadays, so I must stay continuously vigilant to keep the Forum clean. You should now see the download link. Sorry for the inconvenience.

Best regards,

Xiang-Jun