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Messages - febos

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26
I'm sorry this numbers was not from PDB but from the output:
 156  155  0 #   39 | A:.171_:[..G]G-----C[..C]:.155_:A  2.13  0.21 41.31  7.67  1.05
 157  154  0 #   40 | A:.172_:[..C]C-----G[..G]:.154_:A  1.14  1.05 36.08  8.79  1.74
 158  153  0 #   41 | A:.173_:[..G]G-----C[..C]:.153_:A  1.71  0.64 14.01  8.98  1.49
 159  152  0 #   42 | A:.174_:[..C]C-----G[..G]:.152_:A  0.91  0.16 13.88  9.06 -0.28
 160  151  0 #   43 | A:.175_:[..G]G-----C[..C]:.151_:A  1.08  0.08 18.94  8.86 -0.26
 161  150  0 #   44 | A:.176_:[..G]G-----C[..C]:.150_:A  0.47  0.38 12.90  8.88 -0.27
 162  149  0 #   45 | A:.177_:[..G]G-**+-A[..A]:.149_:A  7.09  0.33 10.03  9.49  7.75

I also thought you know what hairpin loop is, i don't know why, I'm sorry.

Quote
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures.
http://en.wikipedia.org/wiki/Stem-loop
And this is an example picture:

Oh, and I was using 3DNA ver 1.5.


27
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?

28
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?

29
Thank you for the detailed explanation, it was very useful. I attached the list of pdb files with similar cases. I'm not sure about all of them, but at least the most part of these contain the same problem as 1Z58.pdb. All of these files contain ribosomal rna.

30
Thank you again for your detailed answer. I attached file 1Z58.out1. In this output bps with numbers 148  (pdb numbers of nucleotides 337-347) and 149 (338-346) are in one helix. But there is another bp with number 130 (348-336) and this bp is a part of another helix. So i thought pairs 336-348, 337-347 and 338-346 must compose a helix, why it isn't?. I hope this time I was enough specific.

31
Thank you for so quick answer. I think i didn't posed my question correctly. I understand what letters "+ | x" mean, but i'd like to know why the program says so. For example i attached a pdb file 1AJU.out5. This is the output of find_pair to model 5 of 1aju.pdb structure. As you can see the helix is made up of bps from 1-30 to 13-20. and pairs 15-18 and 16-17 are isolated. But all these bps don't conflict with each other and don't have any other problems so why the last ones aren't in helix? Is it because they consist of non-WC bonds?
While I was writing this text I remembered another issue. When bp is represented with bigger number first (like 20-9) does it mean anything?

32
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], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.