Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.


Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Download/Licensing · {Video Overview of DSSR}

Messages - mauricio esguerra

Pages: 1 [2]
26
MD simulations / Re: Interpretation of Analysis data from 3DNA
« on: February 25, 2012, 02:06:09 pm »
Hi,

It seems like you have only run find_pair.
You now have to run analyze to get the output file with rigid-body parameters and more.

Code: [Select]
analyze normal_10ns.inp
analyze modified.inp

This will produce the output files normal_10ns.out and modified.out.

I suggest looking at the documentation (e.g. x3dna_v1.5.pdf) which you can find in the doc folder.

27
Bug reports / Re: Problems using fiber in version 2.1 -- 2012
« on: February 23, 2012, 03:54:34 am »
Hi Xiang-Jun,

Thanks.
Problem fixed with fiber-2  :-)

Here's the verbatim copy of running both commands:

Code: [Select]
fiber-1 -a -seq="aattgg" fa-1.pdb
Fiber data in directory: /Users/esguerra/Software/X3DNA2.1/fiber/

 ...... /Users/esguerra/Software/X3DNA2.1/config/ ......
 ...... reading file: misc_3dna.par ......
Structure #1; Twist: 32.7 (degrees); Rise: 2.548 (Angstrom)
fiber dir: str01/
structure: str01/A.rpt
open_file <str01/A.rpt> failed: No such file or directory

And for the working version I get the  fa-2.pdb output as expected.

Code: [Select]
=>fiber-2 -a -seq="aattgg" fa-2.pdb
Fiber data in directory: /Users/esguerra/Software/X3DNA2.1/fiber/

 ...... /Users/esguerra/Software/X3DNA2.1/config/ ......
 ...... reading file: misc_3dna.par ......
Structure #1; Twist: 32.7 (degrees); Rise: 2.548 (Angstrom)

Thank you very much,

Mauricio

28
Bug reports / Re: Problems using fiber in version 2.1 -- 2012
« on: February 22, 2012, 08:32:45 am »
Hi Xiang-Jun,

Here's the output I get from the commands you suggest:

Code: [Select]
echo $3DNA
/Users/esguerra/Software/X3DNA2.1

Code: [Select]
ls $X3DNA/fiber
data    str05  str11  str17  str23  str29  str35  str41  str47  str53
README  str06  str12  str18  str24  str30  str36  str42  str48  str54
str01   str07  str13  str19  str25  str31  str37  str43  str49  str55
str02   str08  str14  str20  str26  str32  str38  str44  str50  str901
str03   str09  str15  str21  str27  str33  str39  str45  str51
str04   str10  str16  str22  str28  str34  str40  str46  str52

I have fedora 14 64bit version.

29
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

30
Ohh...! Great!
I usually pay attention to the forum but I didn't see this one.
Thanks!

Mauricio

31
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

32
General discussions (Q&As) / Re: constructing a modified sugar
« on: September 26, 2011, 07:53:44 am »
Hi,

If what you want is to make your nucleic acid with some favorite step parameters and then modify the sugars to LNA, then I suggest using Accelerys Discovery Studio 3.1 Visualizer (ADS), which is free for academics.
That is, you make the non-LNA in 3DNA, and then you open it with ADS which allows you to modify the sugars an leave everything else intact.
It's also nice if you wanna do MD runs with CHARMM, since it allows you to save in crd and psf format which CHARMM needs to run.

Cheers,

M.

33
Dear Dr. Lu,

Thanks a lot for taking the time to dig into your old records and putting this together.
I have done my data processing using R instead of matlab, which is nice to use since it has a very active community of developers constantly adding a lot of functionality and graphic "eye-candy". As soon as I sort out the details that I was having trouble with on reproducing your results from your PNAS98 paper I will follow your example and post a tar.gz file here with the R code.

Thanks once more,

Mauricio

34
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

35
General discussions (Q&As) / Re: findpair -p and -z options
« on: March 13, 2010, 02:07:36 pm »
Hi,

Perhaps you are already aware of Yurong Xing's database on RNA base-pairs?, if not, it might be useful to you.
You can find it at:

http://http://bps.rutgers.edu

You can search by PDBID, or NDBID if you go to:

http://http://bps.rutgers.edu/search/strid

You can find more information on what the output means, specially the helical region classification at:

http://http://bps.rutgers.edu/bps/help_bp

Hope this helps,

Mauricio

36
Thanks for the fast reply Dr. Xiang-jun,

What I meant by "isolate the base-step" was just that I have a script to pull out to a new structure, say residues G_1709 and A_1711 from the whole ribosomal structure 1jj2, and then I can run 3DNA on this new structure to compute the step parameters that I'm looking for.

Thank you for the advice. I just did it using your advice by separating find_pair -s from analyze, and modification of find_pair output, and it works perfect.

Thanks,

Mauricio

37
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

38
Wow!
Thank you very much. That's great.
I should have checked in my Linux/Unix book about redirectioning first.

Thanks again,

Mauricio

39
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

40
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.

41
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

42
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

43
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]

44
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.

Pages: 1 [2]

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.