Mfold - RNAML output

2 replies [Last post]
Nozdi
Offline
Joined: 07/24/2013

Compiled with gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 and gfortran GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
After using:

mfold SEQ=file_name

I receive all extensions(.ct, .pdf, .ps, .ss, .ann, .det, .gif, .sav, .out, .plot, .pnt) but not .rnaml.

The question is: How can I get .rnaml file from mfold (like on your website)?

Log file (example):
mfold version 3.5 by Michael Zuker
Enter run type
0 Regular run (default)
1 Save run
2 Continuation run

Enter save file name (default fold.sav)

Input sequence file name (q to quit)

Available sequence(s) in seq-local.seq

1) seq

Choose sequence by number [default is 1], or enter F for a new file:

Length of retrieved sequence = 136

seq 136 nucleotides

Enter start of fragment (default 1)
Enter end of fragment (default 136)
Enter asymmetric interior loop of size 3 energy file name
(default asint1x2.dat)
Enter asymmetric interior loop of size 5 energy file name
(default asint2x3.dat)
Enter dangle energy file name (default dangle.dat)
Enter loop energy file name (default loop.dat)
Enter misc. loop energy file name (default miscloop.dat)
Enter symmetric interior loop of size 2 energy file
name (default sint2.dat)
Enter symmetric interior loop of size 4 energy file
name (default sint4.dat)
Enter symmetric interior loop of size 6 energy file
name (default sint6.dat)
Enter stack energy file name (default stack.dat)
Enter tetraloop energy file name (default tloop.dat)
Enter triloop energy file name (default triloop.dat)
Enter tstackh energy file name (default tstackh.dat)
Enter tstacki energy file name (default tstacki.dat)

1 Energy Parameter 7 Double Prohibit
2 Single Force 8 Prohibit Range
3 Double Force 9 Maximum distance
4 Closed Excision 10 Begin folding
5 Open Excision 11 Show current
6 Single Prohibit 12 Clear current

Enter Choice

Energy Parameters (10ths or 100ths kcal/mol)

1 Extra stack energy [ 0]
2 Extra bulge energy [ 0]
3 Extra loop energy (interior) [ 0]
4 Extra loop energy (hairpin) [ 0]
5 Extra loop energy (multi) [ 340]
6 Multi loop energy/single-stranded base [ 0]
7 Maximum size of interior loop [ 30]
8 Maximum lopsidedness of an interior loop [ 30]
9 Multi loop energy/closing base pair [ 40]
10 Helix penalty per non-GC closing pair [ 50]
11 GGG hairpin bonus [ -220]
12 poly-C loop penalty: slope [ 30]
13 poly-C loop penalty: intercept [ 160]
14 poly-C loop penalty: hairpin of size 3 [ 140]
15 Intermolecular initiation free energy [ 410]
16 GAIL Rule - 1 for version 3 rules only [ 1]
Enter Parameter to be changed ( for main menu)
Enter new value

Energy Parameters (10ths or 100ths kcal/mol)

1 Extra stack energy [ 0]
2 Extra bulge energy [ 0]
3 Extra loop energy (interior) [ 0]
4 Extra loop energy (hairpin) [ 0]
5 Extra loop energy (multi) [ 340]
6 Multi loop energy/single-stranded base [ 0]
7 Maximum size of interior loop [ 30]
8 Maximum lopsidedness of an interior loop [ 30]
9 Multi loop energy/closing base pair [ 40]
10 Helix penalty per non-GC closing pair [ 50]
11 GGG hairpin bonus [ -220]
12 poly-C loop penalty: slope [ 30]
13 poly-C loop penalty: intercept [ 160]
14 poly-C loop penalty: hairpin of size 3 [ 140]
15 Intermolecular initiation free energy [ 410]
16 GAIL Rule - 1 for version 3 rules only [ 1]
Enter Parameter to be changed ( for main menu)
Enter new value

Energy Parameters (10ths or 100ths kcal/mol)

1 Extra stack energy [ 0]
2 Extra bulge energy [ 0]
3 Extra loop energy (interior) [ 0]
4 Extra loop energy (hairpin) [ 0]
5 Extra loop energy (multi) [ 340]
6 Multi loop energy/single-stranded base [ 0]
7 Maximum size of interior loop [ 30]
8 Maximum lopsidedness of an interior loop [ 30]
9 Multi loop energy/closing base pair [ 40]
10 Helix penalty per non-GC closing pair [ 50]
11 GGG hairpin bonus [ -220]
12 poly-C loop penalty: slope [ 30]
13 poly-C loop penalty: intercept [ 160]
14 poly-C loop penalty: hairpin of size 3 [ 140]
15 Intermolecular initiation free energy [ 410]
16 GAIL Rule - 1 for version 3 rules only [ 1]
Enter Parameter to be changed ( for main menu)

1 Energy Parameter 7 Double Prohibit
2 Single Force 8 Prohibit Range
3 Double Force 9 Maximum distance
4 Closed Excision 10 Begin folding
5 Open Excision 11 Show current
6 Single Prohibit 12 Clear current

Enter Choice
Enter save file name (default fold.sav)
Enter helix file name
>
vmin = -63.4 Enter energy increment >
Enter number of levels >
Removing non-optimal helices of length less than 2
seq.plot replaced by new file.
Enter save file name (default fold.sav)
Enter p-num file name
>

vmin = -63.4. Enter energy increment >
====> Output file is seq.h-num

mfold version 3.5 by Michael Zuker
Enter run type
0 Regular run (default)
1 Save run
2 Continuation run

Enter run mode
0 Sub-optimal plot (default)
1 n-best
2 Multiple Molecules

Enter percentage for sort (default 0)

Enter number of tracebacks (default 1)

Enter window size (default 0)

Enter save file name (default fold.sav)
Enter file name for continuation dump(return for terminal)
No choices currently defined
Energy Parameters

Energy Parameters (10ths kcal/mol)

1 Extra stack energy [ 0]
2 Extra bulge energy [ 0]
3 Extra loop energy (interior) [ 0]
4 Extra loop energy (hairpin) [ 0]
5 Extra loop energy (multi) [ 340]
6 Multi loop energy/single-stranded base [ 0]
7 Maximum size of interior loop [ 30]
8 Maximum lopsidedness of an interior loop [ 30]
9 Multi loop energy/closing base pair [ 40]
10 Helix penalty per non-GC closing pair [ 50]
11 GGG hairpin bonus [ -220]
12 poly-C loop penalty: slope [ 30]
13 poly-C loop penalty: intercept [ 160]
14 poly-C loop penalty: hairpin of size 3 [ 140]
15 Intermolecular initiation free energy [ 410]
16 GAIL Rule - 1 for version 3 rules only [ 1]

Listing of energy files? (y/N)
Do you want printer output? (Y,n)
Output to terminal? (Y,n)
Enter output file name (default seq.out___________________________________________ )
Do you want ct file? (y,N)
Enter ct file name (default seq.ct ___________________________________________ )
Do you want a detailed ddG table? (y,N)
Enter detailed ddG table file name (default seq.det___________________________________________ )

End reached at traceback 3
boxplot_ng, mfold 3.6
Trying to open seq.plot
The number of helices is 21
Helix total is 22
There are 21 helices in the plot file.
Postscript file name is seq.ps
Creating gif 612 by 792
gif file is seq.gif.
gifdat file is seq.gifdat
Normal exit from boxplot_ng.
CurrentFile= seq-temp_1.ct
CurrentFile= seq-temp_2.ct
CurrentFile= seq-temp_3.ct
Rotation angle: 0.00 degrees
Input File: seq_1.ct
Sequence length: 136
Using 356.0 degrees of the circle
Output: seq_1.ps
ss file output is seq_1.ss
Normal exit from sir_graph.
Rotation angle: 0.00 degrees
Input File: seq_1.ct
Sequence length: 136
Using 356.0 degrees of the circle
Output: seq_1.ps
Normal exit from sir_graph.
Rotation angle: 0.00 degrees
Input File: seq_1.ct
Sequence length: 136
Using 356.0 degrees of the circle
Output: seq_1.png
png File: seq_1.png
png dimensions 792 x 1072
Normal exit from sir_graph.
Rotation angle: 0.00 degrees
Input File: seq_2.ct
Sequence length: 136
Using 356.0 degrees of the circle
Output: seq_2.ps
ss file output is seq_2.ss
Normal exit from sir_graph.
Rotation angle: 0.00 degrees
Input File: seq_2.ct
Sequence length: 136
Using 356.0 degrees of the circle
Output: seq_2.ps
Normal exit from sir_graph.
Rotation angle: 0.00 degrees
Input File: seq_2.ct
Sequence length: 136
Using 356.0 degrees of the circle
Output: seq_2.png
png File: seq_2.png
png dimensions 792 x 1072
Normal exit from sir_graph.
Rotation angle: 0.00 degrees
Input File: seq_3.ct
Sequence length: 136
Using 356.0 degrees of the circle
Output: seq_3.ps
ss file output is seq_3.ss
Normal exit from sir_graph.
Rotation angle: 0.00 degrees
Input File: seq_3.ct
Sequence length: 136
Using 356.0 degrees of the circle
Output: seq_3.ps
Normal exit from sir_graph.
Rotation angle: 0.00 degrees
Input File: seq_3.ct
Sequence length: 136
Using 356.0 degrees of the circle
Output: seq_3.png
png File: seq_3.png
png dimensions 792 x 1072
Normal exit from sir_graph.

Albern43
Albern43's picture
Offline
Joined: 05/26/2016
Ubuntu can be downloaded free on the

Ubuntu can be downloaded free on the authorized website of the organization in ISO format. It can copy to a cd / dvd and then install in a few actual simple steps. A big benefit of Ubuntu is that it can be used without even the hdd install via Live Period. Good Morning Love Quotes

normajane
Offline
Joined: 02/11/2016
In order to easily view,

In order to easily view, analyze, manipulate and save rna data stored in rnaml file format, we have designed a graphical viewer implemented with the Java language. This viewer named RnamlView open a pdb or an rnaml file and construct :
a tree representation of the RnaML file
the rna secondary structure stored in the RnaML file
RnamlView is not able to calculate a secondary structure. It generates a dynamic representation of a secondary structure already stored in an RnaML file.

RnaView is a tool developed at the NDB laboratory (Rutgers University, NJ, USA). It generates a secondary structure from an Rna tertiary structure stored in a PDB file and identifies all the base pairs present in this structure. Therefore, the couple RnamlView-Rnaview allows to easily view and manipulate a Rna tertiary structure. All the base pairs found by RnaView are graphically represented with symbols in agreement with the LW classification.

You can find below a screenshot of RnamlView with :

a tree representation of the RnaML file (1A)
the rna secondary structure stored in the RnaML file (2A)
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