Messages

1

RNA structures (DSSR) / Re: human telomeric g quadruplex - base stacking energy

« on: November 13, 2017, 08:58:12 am »

Dear xiangjun,

I will right now. Thank you a lot!

Best wishes,

Basilio.

2

RNA structures (DSSR) / human telomeric g quadruplex - base stacking energy

« on: November 08, 2017, 10:44:13 am »

Dear Xiang-Jun,


I wonder if 3DNA has an option to calculate the base pair stacking energy (projected area) for g-quadruplex RNA. I know 3DNA can do it for a dsDNA, but I wonder if there is the same option for g-quadruplex.

Thanks you,

Basilio.

3

General discussions (Q&As) / Re: DNA FORM A/B

« on: July 21, 2017, 02:53:37 pm »

I see, I understand. I will also review the source code.Thank you very much.

4

General discussions (Q&As) / DNA FORM A/B

« on: July 21, 2017, 02:10:19 pm »

Dear Dr. Xiang-Jun Lu

I have a question, I could see that in the section Classification of each dinucleotide step in a right-handed nucleic acid
structure: A-like; B-like; TA-like; intermediate of A and B, or other cases. in the output file there is a classification as A like or B-like. However, sometimes I see that the corresponding section appear empty. I copy my output to show you what I mean:

   8 GG/CC   -1.19    8.24    2.31   -9.23    7.09    4.72     A
   9 GG/CC   -1.30    8.29    1.93   -4.17    7.08    4.72     A
  10 GA/TC   -1.49    8.52    1.37   -2.55    8.53    1.31
  11 AG/CT   -1.31    8.33    2.80   -7.37    7.00    5.29     A
  12 GG/CC   -1.10    8.62    2.47   -3.32    8.96    0.43     A

Can you explain, please, what this mean for the software? I mean...I guess this is either not A or not B, what is this?

Thank you very much in advance,

Basilio.

5

General discussions (Q&As) / Re: global DNA curvature analysis

« on: July 17, 2017, 07:18:52 pm »

Really nice paper! Thank you very much!

Best wishes,

Basilio.

6

General discussions (Q&As) / Re: global DNA curvature analysis

« on: July 17, 2017, 04:03:35 pm »

Dear Dr. Xiang-Jun,

I hope this email finds you well. I have a question. I was a following the 3DNA USER GUIDE (http://www.csb.yale.edu/userguides/datamanip/3dna/x3dna.pdf), by the way is very useful, and in page 14 I found this statement: The G+C rich end adopts the A-DNA conformation while the A+T rich part has the B-DNA conformation. As a consequence, this DNA is non-linear, i.e., curved. . Regarding this statement, the USER GUIDE refers to  the work of Pouderoyen et al (1997) but I reviewed the paper and they did not mentioned this statement. I wonder if maybe you can give me a reference about this statement please, to be honest, for my work this information will be very important.

Thank you very much,

Basilio.

7

MD simulations / Re: How to generate a Methylated DNA pdb file from sequence to be use in MD

« on: June 23, 2017, 10:52:57 am »

Dear Xiang-Jun,

Thank you for your soon answer. Sorry if my question was not clear. I was wondering if 3DNA has the option you just mentioned. I could see it does. I will review it right away.

Best wishes,

Basilio.

8

MD simulations / How to generate a Methylated DNA pdb file from sequence to be use in MD

« on: June 23, 2017, 10:31:23 am »

Hello everyone,

I am new in this about MD using nucleic acid and I wonder, maybe this is a silly question, if there is a way to generate a pdb file from my dna sequence where some nucleotides are methylated, also I wonder if there are force field and parameter field available for them.

Thank you very much in advance,
Basilio.

9

MD simulations / Re: "Ruby in cygwin"

« on: April 06, 2017, 10:59:33 am »

Hello

I just installed the new version! I installed the bash on linux on window. Then i installed there ruby and finally 3DNA! Thank you!

Basilio.

10

MD simulations / Re: "Ruby in cygwin"

« on: April 05, 2017, 10:36:41 am »

Hello Xiang-Jun,

I am trying to install the last version of 3DNA(V2.3) in my computer, but I have a problem. My computer is window 10, I am using cygwin. Firstly, I installed ruby using the link you suggested (https://rubyinstaller.org/downloads/) Then I went to the web to download 3DNA v2.3. I download the x3dna-v2.3-mingw-win.tar.gz version. And I followed your advices:

tar pzxvf x3dna-v2.3-linux-64bit.tar.gz
Here the options pzxvf require some explanation:

    p to preserve permissions of the various directories and files. This option may not be required for a personal setting.
    z filter the archive through gzip. With this option, we can work directly from .tar.gz file without first using gunzip.
    x to extract files from an archive.
    v to verbosely list files processed.
    f to use archive file, i.e., the 3DNA tarball file x3dna-v2.3-linux-64bit.tar.gz.

After running the above command, you will get a directory named x3dna-v2.3 which contains the 3DNA v2.3 distribution.
cd x3dna-v2.3/bin
enter into the bin directory of the 3DNA v2.3 distribution.
./x3dna_setup

However, when I ran the last command I got the next error message:

/usr/bin/env: ‘ruby’: No such file or directory

But I just installed ruby.

Just in case, I download the linux version (x3dna-v2.3-linux-64bit.tar.gz) and I tried to install it in cygwin....but I got the same message. I will appreciate your advice,

Thank you,

Basilio.

11

General discussions (Q&As) / Minor and major grove calculation

« on: April 04, 2017, 11:02:42 pm »

Dear Xiang-Jun,

I would like to understand why I got this output when I calculated the minor and major groove from my pdb. It seems that there is some miss values. I attached the pdb I used (I am using 3DNA v2.0)

Thanks you in advance,

Basilio.

                  Minor Groove        Major Groove
                 P-P     Refined     P-P     Refined
   1 AA/TT       ---       ---       ---       ---
   2 AA/TT       ---       ---       ---       ---
   3 AA/TT       9.2       ---      20.8       ---
   4 AA/TT       9.2       9.1      21.1      21.1
   5 AA/TT       9.6       ---      20.1       ---
   6 AA/TT       ---       ---       ---       ---
   7 AA/TT       ---       ---       ---       ---
   8 AA/TT       ---       ---       ---       ---
   9 AA/TT       ---       ---       ---       ---
  10 AA/TT       ---       ---       ---       ---
  11 AA/TT      10.9       ---      19.3       ---
  12 AA/TT      10.6      10.3      18.7      18.4
  13 AA/TT       9.9       9.7      19.5      19.2
  14 AA/TT      10.4      10.3      20.7      20.7
  15 AA/TT      10.6       ---      18.7       ---
  16 AA/TT       ---       ---       ---       ---
  17 AA/TT       ---       ---       ---       ---

12

General discussions (Q&As) / Re: Analysis of dna shape in methylated DNA

« on: April 04, 2017, 10:49:58 pm »

Ah ok, this is the pdb file. Sorry, I did not understand you in the beginning. The version of 3DNA I am using is 3DNA v2.0. I think this is an old version, but I could not install the new one in my computer in window. I will try tomorrow since the actual version I am using cannot analysis MD trajectories.

Best,

Basilio.

13

General discussions (Q&As) / Re: Analysis of dna shape in methylated DNA

« on: April 04, 2017, 09:10:14 pm »

Ok, I understand. Ok, here I go:

Regarding the propeller twist, we can calculate this parameter even when the residue is modify. In my case, methylated cytosine. Since the methylation did not affect the atoms used to calculate the propeller twist, we can use 3DNA to calculate the propeller twist in this residue.

In the beginning I received the message of error because my methylated residue (cytosine) was named as DM in my pdb file. However, it seems that 3DNA just recognize the next names DA,DT,DC and DG. Then I just changed the name DM by DC in my pdb file and the software worked without problem. I hope it can be helpful for other persons.

Best,

Basilio.

14

General discussions (Q&As) / Re: Analysis of dna shape in methylated DNA

« on: April 04, 2017, 08:46:17 pm »

Hi Xiang-Jun,

Thank you for your soon answer. I would be happy to share it, but I would like to know what do you mean when you say "please provide a reproducible example so other can see exactly where the problem is". This means that my solution is correct? and I have to post it?

Thank you,

Basilio.

15

General discussions (Q&As) / Analysis of dna shape in methylated DNA

« on: April 04, 2017, 08:30:33 pm »

Hello,

I hope this email finds you well. I have a question. I got some DM trajectories of methylated GC dsDNA. When I tried to use the command "find_pair mypdb stdout | analyze" to calculate shape parameters I received the next message: unknown residue  DM    2  on chain A [#2]. Then what I did is to change the name (in mypdb) of the residue from DM to DC (Because the DM is methylated cytosine) and the command ran without problem. My logic was that since the methylation is not affecting the base pair, and I am interested to get the propeller twist, I can get correct values of the propeller twist. Is this correct?

Thank you,

Basilio.

16

General discussions (Q&As) / Re: Standards on defining nucleic acid structural parameters

« on: April 02, 2017, 12:53:48 pm »

I see...I understand. Well I can try to calculate them again (because the crystal structures are listed in the table) and see the difference between. I will post what I find just in case someone else need it.

Thank you,

Basilio.

17

General discussions (Q&As) / Re: Standards on defining nucleic acid structural parameters

« on: April 02, 2017, 12:39:08 pm »

Dear Xiang-Jun,

Thank you for your soon answer. I found the paper, and I found the table. I could see there is not a difference between a pair A-T and G-C. I wonder if this is because they analyzed separately the propeller in A-T and G-C, but they did not find difference or they just calculated the average propeller twist for all the structures. Well I just wanted to share this doubt with you. I will read in detail the paper.

Thank you so much,

Basilio.

18

General discussions (Q&As) / Re: Standards on defining nucleic acid structural parameters

« on: April 02, 2017, 11:59:10 am »

Hello,

I have been reading your post about Standards on defining nucleic acid structural parameters, regarding this I have a question. There is also a standard value for this parameters in DNA? For example, in my case I am interested in the propeller twist in DNA. I wonder if there is a standard value of propeller twist for the pair A-T that I can use to compare with my data. I mean for example, I am studying the conformation of a sequence of DNA when interact with a protein...here the pairs A-T could show a value of -20 for example...I wonder is there is a standard value for this pair A-T to compare with my results to calculate a deviation. The same for the other one G-C.

Thank you so much,

Basilio.

19

MD simulations / "Ruby in cygwin"

« on: March 17, 2017, 07:15:59 pm »

Hello! My name is Basilio

I am trying to use 3DNA to analyze some MD data. I tried to do it with x3dna v2.0 (32) but it seems that this option is available just in x3dna v2.3....however, when I tried to install this in cygwin64...everything was ok till the computer told me that the problem is 'RUBY' I tried to install it but I did not find how to install ruby in cygwin64.... i really will appreciate your advice

Thank you,

Basilio.

20

General discussions (Q&As) / "Running 3DNA in cygwin64"

« on: March 16, 2017, 07:41:18 pm »

Hello,

I am Basilio Cieza. I have a question. I download 3DNA without problems, I download cygwin64 already and I followed the steps you suggested in a previous related question (http://forum.x3dna.org/howtos/how-to-install-3dna-on-cygwin-windows/msg2288/#msg2288) which suggest that everything is going well. However, I do not know if the installation was correctly done or not. I try to follow this manual (http://www.csb.yale.edu/userguides/datamanip/3dna/x3dna.pdf) but it seems that the commands like "find_pair pde0128.pdb pde0128.inp" are not working. I receive the message the command does not exist when I tried  to run it. I will really appreciate your advice.

Thank you so much,

Basilio