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Topics - febos

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1
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

2
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:
Quote
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

3
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

4
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

5
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

6
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

7
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

8
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.

9
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.

10
RNA structures (DSSR) / a little note about DSSR installation
« on: November 16, 2013, 01:37:15 am »
Good Afternoon Dr. Xiang-Jun Lu.

Thanks for your new program. Before it i was using find_pair in my RNA research, but DSSR seems quite better for me.

I want to tell You about a little problem with installation:

I have Windows 7 (x86) and when I downloaded x3dna-dssr and tried to run it i have got an error message. I don't remember the full text but it was about missing Cygwin1.dll. So i just copied this dll from my x3dna folder to folder with x3dna-dssr and it worked fine. So my message is not a bug report, but I just want to attract Your attention since You claim that DSSR is self-contained, that's all. Sorry if I missed an explanation of this problem, but I've read all relating DSSR posts at this forum.

Best regards,
Eugene.

11
Good afternoon, mr. Xiang Jun. I have one more question. Yesterday I was looking at different outputs of find_pair and I found this:

A 149 A 162 A-+**-G 
A 150 A 161 C-----G 
A 151 A 160 C-----G 
A 152 A 159 G-----C 
A 153 A 158 C-----G 
A 154 A 157 G-----C 
A 155 A 156 C-----G

This region represent a hairpin loop of length zero (between 155 and 156). But I know that such things don't exist in the real life. This region was found in file 3UZN.pdb. Can you say something about it?

12
I'm sorry, but I don't have a list of problematic helices for these files. But, instead, I have a new question for you :). Could you please explain what symbols '*' and '+' mean in descriptions of bonds (for example 'U-**+-G')?. Again, I'm sorry if this question had been already discussed. I need to know which bonds can roughly be considered as WC-pairs. For example which of these pairs: A-*---U;A-**--U; A-**+-U - can I consider as A-----U?

13
Hello, my name is Eugene. I'm using the X3DNA v 1.5 "find_pair" feature in my research (example of using: "find_pair -t xxxx.pdb xxxx.out"). So, i don't understand how the program marks helices and isolates. As I know "+" is for isolated bps and "|" or "x" are for helices. So could You pleace explain to me what helices and isolates marked by this program exactly mean? I'm sorry if this question has already been discussed. And also excuse me for my english. Thank you.

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Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.