Messages

1

Site announcements / Re: Clarification on DSSR licensing

« on: August 11, 2022, 07:34:37 am »

Hi Dr. Lu!

About two years ago I downloaded DSSR version 2.0 for academic use and since then I built some work using the tool. Only now have I found out that the newest DSSR versions are not freely available anymore. And now I have a question - is it safe to freely use the old DSSR version for academic use according to the old license?

Thank you!

Best regards,
Eugene Baulin

2

RNA structures (DSSR) / Classical RNA loop motifs

« on: July 19, 2021, 04:00:41 am »

Dear Dr. Lu,

As I understand correctly, for the moment there is no program (or database) that annotates (or stores) classical RNA loop motifs explicitly.
By the classical RNA loop motifs I mean sarcin/ricin loop, E-loop, tandem sheared G-A, GA/AAG internal loop, UAA/GAN internal loop, kink-turn, etc.

As I know it:
1) only kink-turns are annotated by DSSR.
2) for sarcin/ricin loop, E-loop, and tandem sheared G-A the best way of annotation is to use manually curated annotation from RNAMotifContrast and merge it with the RNA Motif Atlas clusters' identifiers.
3) for GA/AAG internal loop and UAA/GAN internal loop annotation there are no existing ways at all.

If I'm wrong, could you please let me know if I missed anything?
If I'm right, are there any plans to add the mentioned motifs to DSSR functionality in the future?

Thanks in advance!

Best regards,
Eugene Baulin

3

RNA structures (DSSR) / Re: DSSR multiplets

« on: October 08, 2017, 02:25:35 pm »

Dr. Lu,

That's it! Thank you!

Respectfully,
Eugene

4

RNA structures (DSSR) / Re: DSSR multiplets

« on: October 08, 2017, 12:15:49 pm »

Dr. Lu,

I'm sorry for not being clear. By "aligned" I mean that if I take several base triples from an arbitrary dssr-multiplets.pdb file and look at them in Jmol - they appear aligned. So my question is about processing coordinates of the nucleotides - the coordinates of nucleotides in dssr-multiplets.pdb are different from initial PDB entry. Could you please explain what transformation DSSR performs in there?

Respectfully,
Eugene

5

RNA structures (DSSR) / DSSR multiplets

« on: October 08, 2017, 10:57:50 am »

Dear Dr. Lu,

At the moment I study RNA base triples found in RNA-containing PDB entries using DSSR. I and my students have created a new classification of base triples with respect to secondary structure environment of their nucleotides and now we are planning to implement the classification within our database's web-interface.
We thought it would be helpful to include the 3D visualization of an arbitrary set of aligned base triples and while working on that problem I've noticed that DSSR stores aligned base triples within its output file named dssr-multiplets.pdb.
Could you please tell me how you align multiplets in DSSR? Unfortunately I couldn't have found this information in DSSR tutorials.

Thanks in advance.

Respectfully,
Eugene

6

RNA structures (DSSR) / Re: "malloc failure"

« on: February 01, 2017, 12:45:47 pm »

Good afternoon, Dr. Lu

At first i have not thought about memory since problematic entries were not the largest ones. Now I understand that when i run DSSR i have had some other heavy processes running. I tried to stop them and run DSSR on 5tgm again. It worked just fine.
Thank you and please sorry for bothering.

Eugene

7

RNA structures (DSSR) / "malloc failure"

« on: January 31, 2017, 08:33:37 am »

Good afternoon, Dr. Lu

i have found a problem with some pdb entries (around 50 different entries).
For example:
entry 5tgm:

x3dna-dssr-170122 -i=5tgm.cif1 --idstr=long --more -o=5tgm0122.out1

Processing file '5tgm.cif1'
allocate_atoms_array(): malloc failure (411589)

Time used: 00:00:00:05

this problem holds within at least three last versions of DSSR (17jan22, 16nov19, 16oct19).

Could you please explain this issue?

thanks in advance,
Eugene

8

RNA structures (DSSR) / Re: non-one-char chain identifiers

« on: January 25, 2016, 08:13:10 am »

Good afternoon, Dr. Lu

Sorry for late reply.
This fix should be great.

Just in case:
In pdb entries I saw chain identifiers up to 4 chars (I do not know if it can be longer or not, but 4 is the largest I have seen).
Does the last update of DSSR take it into consideration?

Best regards,
Eugene

9

RNA structures (DSSR) / non-one-char chain identifiers

« on: January 24, 2016, 12:45:05 pm »

Good afternoon, Dr. Lu

I've noticed an issue with long chain identifiers in the section with dot-brackets.

Example:
Entry - 1VY6

fragment from DSSR output header:

Code: [Select]

no. of DNA/RNA chains: 12 [AA=1498,AV=13,AW=2,AX=76,BA=2819,BB=120,CA=1503,CV=12,CW=2,CX=76,DA=2800,DB=120]fragments from dbn section:

Code: [Select]

>1vy6-1-A #1 nts=1498 [chain] RNA*
>1vy6-1-A #2 nts=13 [chain] RNA
>1vy6-1-A #3 nts=2 [chain] RNA
>1vy6-1-A #4 nts=76 [chain] RNA
>1vy6-1-B #5 nts=2819 [chain] RNA*
>1vy6-1-B #6 nts=120 [chain] RNA
>1vy6-1-C #7 nts=1503 [chain] RNA*
>1vy6-1-C #8 nts=12 [chain] RNA
>1vy6-1-C #9 nts=2 [chain] RNA
>1vy6-1-C #10 nts=76 [chain] RNA
>1vy6-1-D #11 nts=2800 [chain] RNA*
>1vy6-1-D #12 nts=120 [chain] RNA
I cannot recover one-to-one correspondence from these lines. I mean, of course in the given case i am able to find correspondence not from identifiers but from lengths, but this is just a lucky example.
Could you fix this, please?


Best regards,
Eugene

10

RNA structures (DSSR) / Re: Strange bp parameters in 1FFK

« on: November 06, 2015, 11:14:47 am »

Dr. Lu,

Thank you for your explanation.
I will read those blog posts and the article of Richardson.
I think I will be able to understand the difference between two sets of parameters after that.

Best regards,
Eugene

11

RNA structures (DSSR) / Strange bp parameters in 1FFK

« on: November 05, 2015, 03:33:58 am »

Good Afternoon, Dr. Lu.

I've noticed some strange numbers in the 1st bp in the 1FFK file (in pdb format):

Code: [Select]

   nt1            nt2           bp  name        Saenger    LW  DSSR
   1 .0.U.12.       .0.G.531.      U-G --          n/a       tHS  tM-m
       [-171.2(anti) ~C3'-endo lambda=8.4] [-159.4(anti) ~C3'-endo lambda=97.9]
       d(C1'-C1')=10.93 d(N1-N9)=9.76 d(C6-C8)=10.33 tor(C1'-N1-N9-C1')=-76.3
       H-bonds[1]: "O4(carbonyl)-N2(amino)[2.99]"
       interBase-angle=12  Simple-bpParams: Shear=-7.49 Stretch=3.77 Buckle=-5.4 Propeller=10.8
       bp-pars: [-7.75   -3.20   0.40    -11.69  2.97    -4.39]
in all other basepairs there is a respectivity (is it a right word?) between "Shear=" and №1 of "bp-pars"; "Stretch=" and №2; "Buckle=" and №4; "Propeller=" and №5.
But in this bp there is no such thing. Do I missing something or it is in fact a bug? And which parameters are actually real?

Best regards,
Eugene

12

RNA structures (DSSR) / exotic CIF format

« on: September 06, 2015, 07:53:49 am »

Good Afternoon!

I'd like to draw Your attention to structure 5AJ0 (http://www.rcsb.org/pdb/files/5AJ0.cif).
Its mmCIF file contains exotic row orderings in its tables and DSSR is not capable to parse it in right way.
For instance, in its "_atom_site" table words "ATOM/HETATM" are not first words in line.

Best wishes
Eugene

13

RNA structures (DSSR) / Re: Non-standard alternate location indicator

« on: May 06, 2014, 12:24:14 pm »

Good afternoon Dr. Xiang-Jun Lu

I want to report some unusual behaviour of DSSR (latest version - Apr 19)

If I run DSSR without option --altloc=smth on pdb-file in which this option is needed - the console ouput looks something like " no ATOM/HETATM entries found. Time used 00:00:00" and out-file isn't created. But: in the latest version in this case my script gets from DSSR returnvalue=0 (there was not any error). In previous versions (particularly jan 25) my script got returnvalue=1 in such cases (program finished with error).

I need to get returnvalue=1 in such cases so my script can identify when --altloc is needed.

Could you please fix this?

Best regards,
Eugene.

14

General discussions (Q&As) / Re: What other software is available?

« on: February 05, 2014, 01:21:46 am »

Thanks, Dr. Lu

15

General discussions (Q&As) / Re: What other software is available?

« on: February 04, 2014, 09:24:03 am »

Good Afternoon Dr. Lu.

Do you know any tools or programs which are similar to DSSR? (Especially for determining base-pairs from pdb-file).
DSSR is great for me but I need to know that it's the best and so far I could not find other programs.

Best regards,
Eugene

16

RNA structures (DSSR) / Re: Question on Multiplets

« on: January 29, 2014, 12:38:41 am »

Dr.Lu,

I looked at this file in Jmol and now I understand Your definition.

Thanks for Your help.

Best regards,
Eugene

17

RNA structures (DSSR) / Question on Multiplets

« on: January 28, 2014, 01:10:51 pm »

Good Afternoon, Dr. Lu

I found out that multiplets in DSSR (beta-r29-on-20140106) can intersect each other, example in 2RSK (model 8 ):

Code: [Select]

****************************************************************************
List of 4 multiplet(s)
   1 nts=4 GGGG [8.A.G.2.+8.A.G.5.+8.A.G.8.+8.A.G.11.]
   2 nts=4 GGGG [8.B.G.14.+8.B.G.17.+8.B.G.20.+8.B.G.23.]
   3 nts=7 GAGAGAG [8.A.G.1.+8.A.A.3.+8.A.G.4.+8.A.A.6.+8.A.G.7.+8.A.A.9.+8.A.G.10.]
   4 nts=10* AAAGAGAGAG [8.A.A.3.+8.A.A.6.+8.A.A.9.+8.B.G.13.+8.B.A.15.+8.B.G.16.+8.B.A.18.+8.B.G.19.+8.B.A.21.+8.B.G.22.]

****************************************************************************Here nts 8.A.A.3.;8.A.A.6.;8.A.A.9. are in both №3 and №4 multiplets.

Considering this issue I'd like to know what is Your definition of Multiplet? And also what does symbol "*" in " nts=10* " mean?

I'm sorry if You already described it somewhere else.

Best regards,
Eugene

18

RNA structures (DSSR) / Re: Request for comments on DSSR output before v1.0 release

« on: January 14, 2014, 05:09:47 am »

Hi Dr. Lu.

I want to report a little issue:

when I run dssr on 1FFK i see following info:

Code: [Select]

Processing file '1FFK.pdb1' [1FFK]

total number of base pairs: 1406
total number of multiplets: 219
total number of helices: 104
total number of stems: 175
total number of hairpin loops: 66
total number of bulges: 34
total number of internal loops: 63
total number of junctions: 31
total number of non-pairing interactions: 2288
total number of non-loop single-stranded segments: 47
total number of kissing loops: 1
total number of A-minor (type I and II) motifs: 93
total number of ribose zippers: 41 (237)
total number of kink turns: 6
total number of phosphate interactions: 641

Here I don't see number of U-turns however there are 28 U-turns in this pdb-file.

I used commands:

Code: [Select]

x3dna-dssr -i=1FFK.pdb1 -o=1FFK.out1 -note -more -non-pair -u-turn -po4 -break-symbol -long-idstr and

Code: [Select]

x3dna-dssr -i=1FFK.pdb1 -o=1FFK.out1 -u-turn,results are identical.

p/s/ out-file is ok, issue are only in command-line output.

Best regards,
Eugene.

19

RNA structures (DSSR) / Re: A bug with missing right-side type bulges

« on: January 10, 2014, 05:51:47 am »

Hi Dr. Lu

I'm glad to help you.

Now it works fine.

Best regards,
Eugene.

20

RNA structures (DSSR) / an issue with bulges

« on: December 24, 2013, 05:57:21 am »

Good Afternoon, Dr. Lu.

I think I've found a real bug with bulges in DSSR:

Bulges can be of two types - "right" ([0xN]) and "left" ([Nx0]).  I looked at all pdb files with RNA and found that in DSSR output there are just 4 cases of right bulges (from about 8500 bulges) and all these 4 cases are bulges between different rna chains! (strand1 - one chain; strand2 - another chain). I'm sorry but now I can't remember in which files these 4 cases were. But the main problem is that DSSR has no proper right bulges!

One example:

file 1FFK, chain 9:

I attached picture of its secondary structure (1FFK_9.png, made with VARNA).

As you can see from picture there are 3 bulges on this structure:

1) .9.A.65.                (right bulge of form [0x1])
2) .9.A.51.+.9.A.52. (right bulge of form [0x2])
3) .9.U.87.                (left bulge of form  [1x0])

I also attached DSSR ouput (1FFK.out1), from which you can see:

bulge number 3 ([1x0]):

Code: [Select]

  12 bulge: 5 nts; [1x0]; linked by [#174, #175]
       .9.G.86.+.9.U.87.+.9.G.88.+.9.C.95.+.9.C.96. [GUGCC]
       1 nts bulge .9.U.87. [U]; .9.G.86.-->.9.G.88. [GUG]
       0 nts bulge ; .9.C.95.-->.9.C.96. [CC]
so far so good
and now bulges number 1 and 2 are in non-loop single-stranded segments section:

Code: [Select]

  93 nts=2 .9.A.51.+.9.A.52. [AA]
  94 nts=1 .9.A.65. [A]
I know that 1FFK is not the only file where right bulges exist, so I think that's a common bug.
I hope my explanation was useful.

Best regards,
Eugene

21

RNA structures (DSSR) / Re: Bug report of DSSR beta

« on: December 03, 2013, 05:28:19 am »

Good Afternoon Dr. Xiang-Jun Lu.

I've noticed a little bug in your program, seems like you forgot an opening bracket ('[') in fields of helices and stems:

Code: [Select]

   2 10.A.G.2.        10.A.C.37.       G-C WC           19-XIX    cWW cW-W
        bp1_pars:      -1.29    -0.35    -0.04    -1.33    -0.11    -5.26]
       step_pars:      -0.60    -1.65     3.04    -1.46    22.01    44.24]
       heli_pars:      -3.36     0.63     2.07    27.31     1.81    49.19]
        bp2_pars:       0.37     0.21    -0.06     1.55     2.78    -7.23]
       C1'-based: rise=3.96     twist=34.6     h-rise=2.19     h-twist=39.1
It's in the latest release of DSSR

Best regards,
Eugene

22

RNA structures (DSSR) / Re: Non-standard alternate location indicator

« on: November 29, 2013, 05:36:25 am »

Thank you Dr. Lu

23

RNA structures (DSSR) / Non-standard alternate location indicator

« on: November 28, 2013, 05:18:26 am »

Good afternoon Dr. Xiang-Jun Lu

I suddenly met a problem with your program.
In my research i need to divide pdb file with more than one model into different files.
for example pdb file 406D contains 4 models so I divide it into 4 files (I attached them).

When I'm trying to run dssr on them I see a quite interesting behavior: files 406D.pdb1 and 406D.pdb3 are processed well, but on files 406D.pdb2 and 406D.pdb4 I have following output:

Code: [Select]

x3dna-dssr -i=406D.pdb2 -o=out/406D.out2 -long-idstr
File <406D.pdb2> contains NO ATOM/HETATM records
...exiting...

Time used: 00:00:00:00


but as you can see from attachment my files are practically identical
What could it be?

For more examples I've also attached files 1ZEV.pdb1 and 1ZEV.pdb2 (first was processed well, second had the same problem)

Best regards,
Eugene.

24

RNA structures (DSSR) / Re: what does helix-form mean?

« on: November 22, 2013, 05:45:09 am »

Thank you! Your explanation was very useful for me.

25

RNA structures (DSSR) / what does helix-form mean?

« on: November 21, 2013, 12:20:05 pm »

Good afternoon Dr. Xiang-Jun Lu

Could you please explain to me what does helix-form mean and how do you create it?

Some examples:

Code: [Select]

strand-1 5'-ACC-3'
 bp-type    |||
strand-2 3'-UGG-5'
helix-form  .A

strand-1 5'-GACGGACAAGUU-3'
  bp-type    |||...|||||.
strand-2 3'-CUGAAAGUUCGA-5'
helix-form  A...xx.AAAx

strand-1 5'-CCGUAU-3'
 bp-type    ||||||
strand-2 3'-GGCAUG-5'
helix-form  AAA..

strand-1 5'-CC-3'
 bp-type    ||
strand-2 3'-GG-5'
helix-form  .

strand-1 5'-CCACCGUAUACCG-3'
  bp-type    ||.|||||||||.
strand-2 3'-GGUGGCAUGUGGC-5'
helix-form  ...AAA..x.A.

strand-1 5'-GGC-3'
 bp-type    |||
strand-2 3'-CCG-5'
helix-form  AA

strand-1 5'-CAAGU-3'
 bp-type    |||||
strand-2 3'-GUUCG-5'
helix-form  .AAA

strand-1 5'-UCUG-3'
 bp-type    ||||
strand-2 3'-AGAC-5'
helix-form  A.A

strand-1 5'-CCC-3'
 bp-type    |||
strand-2 3'-GGG-5'
helix-form  ..

Best regards,
Eugene.