Messages

1

RNA structures (DSSR) / create a multiple copy from a building block with DSSR-pro

« on: January 28, 2022, 11:23:34 am »

Hello Dr. Lu,

I am using the DSSR-pro and the work flow you provided to create a multiple copy of a 3bp RNA (attached), I was wondering if it is possible to use the DSSR to create the lost backbone connections.

Thanks,
Amir

x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb

x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair -o=ref-conn.pdb

x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb' -o=temp1.pdb

x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair -o=temp2.pdb
x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb

x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb' -o=duplicate-model.pdb

2

RNA structures (DSSR) / error in rebuild command

« on: May 05, 2021, 04:27:42 pm »

Hello Dr. Xiangjun,

following the example in "np_recipes/R2_roll_bending" I am trying to use the rebuild command to create an image like those provided (Figure3_r300.png) for my RNA systems which are highly bent.

After preparing the input file to execute the following commnad:
 rebuild roll_a.dat roll_a_raw.alc
I receive an error message: unknown residue slide

so I just ran the same command on the example file provided in the "R2_roll_bending" dir (roll_a.dat) and I get the same error message.

I was wondering if I could use your help.

Thanks in forward.

Best,
Amir

3

RNA structures (DSSR) / force DSSR to treat the loop region as base-pairs

« on: April 11, 2021, 05:13:23 pm »

Hello Dr. Xiang-Jun,

I am using the DSSR to analyze a RNA structure (54 bps) with multiple repeats of (AUUCU) seq incorporating multiple 3x3 internal loops. As the structure is highly dynamic, many of the loops do not satisfy the conditions needed to be treated as a base-pair and naturally are skipped by the DSSR.
is there any way, other than manipulating the parameters which are used in DSSR to account for a base-pair, to force the DSSR to analyze all the 54 base-pairs irrespective of the defined criteria for base-pairs.

Thanks for your help.

Best,
Amir 
   

4

General discussions (Q&As) / create RNA sequence syn nucleosides

« on: August 09, 2019, 07:00:14 pm »

Hello,
 
I have a question and I was wondering if you could help.
I want to make a small RNA with the sequence 5' UCAA*GA with the complementary seq. as 3' AGUC*CA. I want to make all four possible combinations of this sequence with the starred  nucleosides (A* and C*) being in the syn-syn, syn-anti, anti-syn & anti-anti (which is the standard form with fiber).
Is there any way that I can create these systems with x3dna.

Thanks in forward.

Best regards,
Amir

5

RNA structures (DSSR) / Re: --nmr option with --get-hbond & --analyze

« on: July 27, 2019, 09:20:30 am »

Thanks a lot, the ensemble option works for --json. Although data extraction was easier with standard x3dna out put (like what I get in stacking with the --nmr  --non-piar combination).   

Cheers,

6

RNA structures (DSSR) / --nmr option with --get-hbond & --analyze

« on: July 26, 2019, 07:23:15 pm »

Hello Dr. Xiang-Jun,

I have a pdb file which contains 100 frames. I have used the --non-pair option with --nmr to analyze all frames and got the output for each frame but using the same combination of commands for --get-hbond & --analyze dose not work with --nmr.

The command is:
x3dna-dssr -i=comb.pdb --get-hbond --nmr -o=Hbonds_analysis.dat

--get-hbond is overwritten by --nmr and no H-bond analysis is done (the same with --analyze). So the following is the header of stacking analysis:

Command: x3dna-dssr -i=md_comb.pdb --non-pair --nmr -o=stacking_analysis.txt

File name: md_comb.pdb
...

and the following is for H-bond analysis:     

Command: x3dna-dssr -i=md_comb.pdb --nmr -o=Hbonds_analysis.txt
Date and time: Fri Jul 26 18:50:59 2019
File name: md_comb.pdb

though I have used the --get-hbond option it does not appear in the output provided by DSSR and no h-bond analysis is done.

So I was wondering if you could help me with my problem.

Thanks in forwrad.
Amir
   

7

General discussions (Q&As) / Re: locked nucleic acids/fiber

« on: July 03, 2019, 02:42:51 pm »

Dear Prof. Xiang-Jun,

So, I made a small change in your script so that I could  remove the nucleotide ('A') which I wanted to replace with 7AL and then loaded both structures (7AL-refOK-fit.pdb and RNA-fiber-ref5.pdb) in pymol and saved it as a single file.
then I loaded the pdb file in xleap (as I have already added the 7AL parameters to the library) and the missing bond was fixed to get the final structure.
your script was very helpful and I learned a lot. I wish there was a few such scripts which could help to better understand the powerful tools of 3DNA.   
again thanks a lot for your help.

Cheers,

8

General discussions (Q&As) / Re: locked nucleic acids/fiber

« on: July 03, 2019, 12:29:50 pm »

Thanks a lot for your help and time. I am trying to use the combination of chimera and xleap (amber) to make the structure as I don't have access to maestro. I will also try DSSR see if I can make it work (thanks for the script). I appreciate your help and time.

Best regards,

9

General discussions (Q&As) / Re: locked nucleic acids/fiber

« on: July 02, 2019, 06:29:32 pm »

Please find attached the pdb file of 7AL. The main changes are that sugar is attached to N7 (instead of N9) and there is a bridge connection between C2', C3' and C4' in the sugar.
I want to make a double stranded RNA which in one strand "A" would be replaced by 7AL ('a') ,UCAGaCAGU, but the second strand remains intact.
Using fiber I have made the dsRNA with the mentioned sequence.

Thanks a lot.

10

General discussions (Q&As) / Re: locked nucleic acids/fiber

« on: July 02, 2019, 05:24:55 pm »

Hi Prof. Xiang-Jun,

Thanks a lot for the reply. So I have a modified locked nucleotide named N7-LNA-adenosine and I want to make the following sequence:
UCAG"7AL"CAGU (I have the geometry optimized pdb file of the 7AL if it is required).
Thanks for your help.

Best regards,

11

General discussions (Q&As) / locked nucleic acids/fiber

« on: July 02, 2019, 04:47:53 pm »

Hello,

I have a question regarding the fiber option of 3DNA. Is it possible to add standard locked nucleotides or user modified ones to the fiber data base so one can create RNA structures which is a mix of standard and locked nucleotides. 
For example I have a regular sequence of "AACGU" and I wand to change the second "A" to "LA", assuming I have the pdb information of "LA".
Thanks in forward for your help.

Best regards,
Amir