Topics

1

General discussions (Q&As) / blocview

« on: June 20, 2018, 08:44:54 am »

Hi Xiang-Jun,

In using blocview I know that the radius of the backbone tube which traces the phosphate atoms can be changed in the last line of the $X3DNA/config/col_chain.dat file.

Nonetheless I would also like to change the radius of the sticks representing the sugar-phosphate backbone bonds.
I can do this manually by altering the resulting .r3d files, say, if one of these bond specifications as a cylinder in raster3D is:

Code: [Select]

3
  -10.965  -18.757   -1.704    0.160   -9.568  -18.592   -1.909    0.160    1.000    1.000    0.000

I can change the 0.160 value in the fourth and eight fields to whichever radius I want.
I was wondering if there's a file where this parameter can be changed in an easier way.

Thanks,

Mauricio

2

RNA structures (DSSR) / cif file compatibility?

« on: May 07, 2015, 10:11:05 am »

Hi Xiang-Jun,

I'm wondering if you have any tips or tricks as to what to do now that the cif format is the official pdb format and giving a lot of us a hard time on adjusting our analysis protocols.
I wanted to use get_part to easily split protein apart from rna in the latest structure of the mitochondrial ribosome from Venkatakrishnan's lab. and I'm having a hard time finding an efficient way to do it.

Any recommendations?

Thank you,

Mauricio

3

General discussions (Q&As) / Details in Zp(h) definition.

« on: February 20, 2013, 10:18:16 am »

Dear Xiang-Jun,

In your cool  and very influential NAR 2003 paper you describe the Zp(h) parameter as:

"Zp(h), equal to half the projection on the local helical axis of the vector, P(II) -> P(I), that links the phosphorus atoms on the two strands forming a given base pair step..."

It appears to me as the only difference between Zp and Zp(h) is that of the election of the reference frame, that is, the middle-frame vs. the local helical axis reference frame.
Is this assumption right?

Thanks for your time on replying to such simple questions,


Mauricio

4

Bug reports / open_file <./Atomic.g.pdb> failed: No such file or directory

« on: October 24, 2012, 05:48:15 am »

Hi Xiang-Jun,

I have just downloaded the latest version of 3DNA dated October 16 for Intel Mac.

I have OS X 10.8.2 (Lion) on a MacBookPro 9.2.

When running find_pair i get the following output:

Code: [Select]

find_pair 1ehz.pdb 1ehz.inp                       ──(Wed,Oct24)─┘

handling file <1ehz.pdb>
uncommon residue 2MG   10  on chain A [#10] assigned to: g
uncommon residue H2U   16  on chain A [#16] assigned to: u
uncommon residue H2U   17  on chain A [#17] assigned to: u
uncommon residue M2G   26  on chain A [#26] assigned to: g
uncommon residue OMC   32  on chain A [#32] assigned to: c
uncommon residue OMG   34  on chain A [#34] assigned to: g
uncommon residue YYG   37  on chain A [#37] assigned to: g
uncommon residue PSU   39  on chain A [#39] assigned to: P
uncommon residue 5MC   40  on chain A [#40] assigned to: c
uncommon residue 7MG   46  on chain A [#46] assigned to: g
uncommon residue 5MC   49  on chain A [#49] assigned to: c
uncommon residue 5MU   54  on chain A [#54] assigned to: u
uncommon residue PSU   55  on chain A [#55] assigned to: P
uncommon residue 1MA   58  on chain A [#58] assigned to: a
open_file <./Atomic.g.pdb> failed: No such file or directory
I thought this was a problem related to not including config in the path and added $X3DNA/config to the path, unsuccessfully.

So 1ehz.inp, with the base-pairing results is not produced as output.

Other commands such as, get_part, work well.

Thanks once more,

Mauricio

5

Bug reports / Problems using fiber in version 2.1 -- 2012

« on: February 22, 2012, 08:03:52 am »

Dear Xiang-Jun,

First of all, thanks for 3DNA V2.1.
The new website and forum are looking great.

I just downloaded and set-up 3DNA V 2.1. and I'm running into the following error when running:
fiber -a ADNA.pdb

open_file <str01/A.rpt> failed: No such file or directory

I have checked my environment variables and they are right.

Thanks once more,

Mauricio

6

General discussions (Q&As) / std_curved parameters seems not to work in 3DNA V2.1

« on: December 01, 2011, 05:45:21 am »

Dear Xiang-Jun,

In previous versions of 3DNA e.g. up to version:
3DNA v2.0 [August 2007] (by Dr. Xiang-Jun Lu; 3dna.lu@gmail.com)

Changing the value of this parameter (i.e. <std_curved>) seems not to affect the analyze program.

I am fine using the August 2007 version for getting the global helical axis, but thought useful to report the bug.

Thanks for devoting so much of your spare time to 3DNA,

Mauricio

7

General discussions (Q&As) / A little background on the -negx option and rebuild of ssRNA

« on: April 13, 2010, 06:05:17 pm »

Dear Dr. Lu,

As you are aware I have been using 3DNA for a while to exclusively analyse RNA structures as in our methods paper.
Right now I am just playing around and reconstructing the ribosome di-nucleotide steps after performing a single stranded analysis of 1jj2.pdb.
Basically what I do is:

1) Get step-parameters.
2) Script to rebuild from rows of step-parameter data (shift, slide, rise, tilt, roll, twist) a separate pdb file for each row/step.

When 3DNA finds a negative twist it reverses the direction of the x- and z-axes.
I would like to ignore this for all cases since I don't have Z-RNA conformations.
Is there another way besides using the -negx command?
Also, I might be missing out the deeper reason for the default behaviour of reversing the axes directions, I understand the reasons for base-pairs as you explain in your NAR paper of 2003 (page 5109), but I don't understand fully the reasons for the step case. Could you please expand a little bit more on this explanation, or point me to some of your papers which I might have overlooked?

Once more, thanks for your always excellent feedback, and for bearing with the newbies in the field like me.

Sincerely,

Mauricio Esguerra

8

General discussions (Q&As) / Finding non-sequential base step parameters

« on: March 08, 2010, 12:17:41 pm »

Hello Dr. Xiang-Jun,

I have been using:
find_pair -s rnastructure.pdb stdout | analyze
to obtain the .outs file which contains the sequential base step parameters for the analysed structure.
I am wondering if it's possible to find all base step parameters, including those which are non-sequential, for example, in the ribosomal structure of pdb:id 1jj2, the bases G_1709 and A_1711 stack in top of each other and therefore their step parameters can be computed, but are not given by default in rnastructure.outs.

I am aware that I can isolate the base_step and calculate the step parameters for them, but I was wondering if it's possible to do without the additional step.

Thanks once again,

Mauricio Esguerra

9

General discussions (Q&As) / Option not to display calculation status to screen.

« on: September 02, 2009, 12:33:37 pm »

Hi Xiang-Jun,

I am running a script for rebuilding a large amount of random dsRNA conformations and then I run find_pair and analyze on the resulting pdb output.
Since I am generating a lot of data I would like to suppress the output to screen because I am sending this to a cluster which generates a bulky error log with the data that find_pair and analyze send to screen.
What I mean more precisely is that if I run find_pair, say:

Code: [Select]

bash# find_pair rna1.pdb stdout | analyze
I get some 3DNA information (output to screen) telling me how the calculation is doing, that is, something like:

Code: [Select]

...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: baselist.dat ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......

Time used: 00:00:00:01

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: baselist.dat ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: baselist.dat ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: misc_3dna.par ......

 ...... /home/esguerra/NFSsoft/X3DNA2/config/ ......
 ...... reading file: raster3d.par ......

Time used: 00:00:00:02
Since I have already checked to see that my output files are right, I don't need this output. I am wondering if there is an internal command to suppress such output.

Thank you,

Mauricio

10

General discussions (Q&As) / How to make blocview -i work with pymol in batch mode.

« on: May 20, 2009, 02:45:48 pm »

Hi Xiang-Jun,

Recently I was using blocview with the -i option to produce ray traced images of a large number of RNA base-steps and found that every time pymol was called, it opened a new OpenGL window (a bit annoying for 100+ molecules).

I thought it would be useful to mention here that to send the OpenGL window to the "background", one just has to alter line 30 of the x3dna_r3d2png script located in the /bin directory of X3DNA to read:

system("pymol -qc $pmlfile 2&> x3dna_r3d_pymol.msg");

instead of

system("pymol $pmlfile 2&> x3dna_r3d_pymol.msg");

Notice that you only need to add -qc after the pymol command.

Hope this helps someone, and thanks for 3DNA Xiang-Jun.

11

General discussions (Q&As) / Silly helical regions question.

« on: October 26, 2007, 02:13:03 pm »

Hello Dr. Xin,

I write again to bother with a similar question that I asked a while ago.
I am wondering if in 3DNA the standard helical regions are the ones that get a poc_haxis.r3d file created, and the ones that do not generate one after running analyze on them are the quasi-continuous ones.

Thanks,

Mauricio

12

Users' contributions / Script to render helical regions as cylindersr

« on: August 16, 2007, 12:58:11 am »

Hello,

I've made a bash script to make my life easier when creating Raster 3D (r3d) files with a cylindrical representation of the straight helical regions found by 3DNA. The script can be found at:

http://eden.rutgers.edu/~esguerra/RNA/scripts.html

The script creates a folder named helical where it will output the r3d file.
The script works only for linux and it needs for 3DNA, raster3D and molscript to be installed.The user only has to put the script in her/his local bin directory, say:

bash> cp gethelireg /home/esguerra/bin

and then the script can be invoked from any folder where one has a pdb file.

bash>gethelireg
Type the name of your pdbfile
1kh6.pdb

Then you just chage directory to helical and you'll find the file 1kh6.pdb.r3d
The script also runs 3DNA's find_pair and analyze automatically using the default arguments of  find_pair and you can find the results in the same folder where you have your pdb coordinates file.

Now, you can just do:

pymol 1kh6.pdb.r3d

And play with the image all you want.

You can get an image like the following using ray_trace_mode in pymol:




Enjoy,

Code: [Select]

#!/bin/bash
# Script to get the helical region files poc_haxis.r3d
# rename them and get them into one single file to be merged with
# the whole skeleton.
echo "Type the name of your pdb file"
read -e INPUT
#find_pair -t  $INPUT stdout | analyze
find_pair  $INPUT stdout | analyze
NUMHEL=`grep "Section #" hel_regions.pdb | tail -n 1 | awk '{print substr($3,2)}'`

mkdir helical
cp $INPUT helical/
cd helical

i="1"
while [ $i -le $NUMHEL ]
do
    echo "$i"
    mkdir rna$i.dir
    ex_str -$i ../hel_regions.pdb rna$i.dir/rna$i.pdb
    cd rna$i.dir
#    find_pair -t rna$i.pdb rna$i.inp
    find_pair rna$i.pdb rna$i.inp
    analyze rna$i.inp
    mv poc_haxis.r3d rna$i.r3d
    cp rna$i.r3d ../
    cd ..
    i=`expr $i + 1`
done
rm -rf rna*.dir
blocview -o $INPUT
echo -e "8 n  17.  0.6       -1.0 -1.0 -1.0     0.4   0 0 0 0" > translucent.r3d
cat t.r3d translucent.r3d rna*.r3d > $INPUT.r3d


13

General discussions (Q&As) / Script for Helical Regions as Cylinders

« on: August 11, 2007, 04:04:43 pm »

Hello,

I've made a bash script to make my life easier when creating Raster 3D (r3d) files with a cylindrical representation of the straight helical regions found by 3DNA. The script can be found at:

http://eden.rutgers.edu/~esguerra/RNA/scripts.html

The script creates a folder named helical where it will output the r3d file.
The script works only for linux and it needs for 3DNA, raster3D and molscript to be installed.The user only has to put the script in her/his local bin directory, say:

bash> cp gethelireg /home/esguerra/bin

and then the script can be invoked from any folder where one has a pdb file.

bash>gethelireg
Type the name of your pdbfile
1kh6.pdb

Then you just chage directory to helical and you'll find the file 1kh6.pdb.r3d

Now, you can just do:

pymol 1kh6.pdb.r3d

And play with the image all you want.

Enjoy,

M.

Code: [Select]


#!/bin/bash
# Script to get the helical region files poc_haxis.r3d
# rename them and get them into one single file to be merged with
# the whole skeleton.
echo "Type the name of your pdb file"
read -e INPUT
#find_pair -t  $INPUT stdout | analyze
find_pair  $INPUT stdout | analyze
NUMHEL=`grep "Section #" hel_regions.pdb | tail -n 1 | awk '{print substr($3,2)}'`

mkdir helical
cp $INPUT helical/
cd helical

i="1"
while [ $i -le $NUMHEL ]
do
    echo "$i"
    mkdir rna$i.dir
    ex_str -$i ../hel_regions.pdb rna$i.dir/rna$i.pdb
    cd rna$i.dir
#    find_pair -t rna$i.pdb rna$i.inp
    find_pair rna$i.pdb rna$i.inp
    analyze rna$i.inp
    mv poc_haxis.r3d rna$i.r3d
    cp rna$i.r3d ../
    cd ..
    i=`expr $i + 1`
done
rm -rf rna*.dir
blocview -o $INPUT
echo -e "8 n  17.  0.6       -1.0 -1.0 -1.0     0.4   0 0 0 0" > translucent.r3d
cat t.r3d translucent.r3d rna*.r3d > $INPUT.r3d

[/code]

14

General discussions (Q&As) / Torsion angles reported from 0 to 360

« on: July 24, 2007, 12:52:44 pm »

Hello,

When I use 3DNA to analyze, say, an 11bp A-RNA as a single strand, one gets the backbone and glycosidic torsion angles in the .outs file. The values range from -180 to 180 degrees. Is there an option to modify the range from 0 to 360 degrees?

I've made a script in R to do the job, but I was just wondering if 3DNA can do such task for you.

Thank you.