Hi Troels,
Additional question that I had, if you could also look into this
as well on Tuesday please. I have decided to try to write a script
to
automate this whole process (since I won't be using the gui to do
model
free), and I've come across a problem. I can successfully open up
relax
using openmpi, and can load the pdb file, and assign all the spins
and
isotopes; however, it appears it will only load one data file (the
very
first one I'll have inputed in the script). I don't know if there
is a
problem with how I wrote my script. Not only will it not load the
rest of
my data sets, it won't actually run dAuvergne's protocol either,
it'll just
load the data set and exit out of the program. Attached is the
script I
wrote for relax.
This is the output once relax has loaded
script = 'model_free_sample_script.py'
------------------------------------------------------------
----------------------------------------
from time import asctime, localtime
from auto_analyses.dauvergne_protocol import dAuvergne_protocol
DIFF_MODEL=['local_tm','sphere','prolate','oblate','ellipsoi
d','final']
MF_MODELS=['m0','m1','m2','m3','m4','m5','m6','m7','m8','m9']
LOCAL_TM_MODELS=['tm0','tm1','tm2','tm3','tm4','tm5','tm6','
tm7','tm7','tm8','tm9']
GRID_INC=11
MIN_ALGOR='newton'
MC_NUM=500
CONV_LOOP=True
pipe_bundle="mf(%s)"%asctime(localtime())
name="origin-"+pipe_bundle
pipe.create(name,'mf',bundle=pipe_bundle)
structure.read_pdb('2d9j.pdb',set_mol_name='hRGS7')
structure.load_spins('@N',ave_pos=True)
structure.load_spins('@NE1',ave_pos=True)
structure.load_spins('@H',ave_pos=True)
structure.load_spins('@HE1',ave_pos=True)
spin.isotope('15N',spin_id='@N*')
spin.isotope('1H',spin_id='@H*')
relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='R2_Agnes',ri_type='R2',frq=599.642*1e6,
file='R2_Agnes',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='ssNOE_Agnes',ri_type='NOE',frq=599.642*1e6,
file='ssNOE_Agnes',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='R1_NMRFAM',ri_type='R1',frq=799.642*1e6,
file='R1_NMRFAM',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='R2_NMRFAM',ri_type='R2',frq=799.642*1e6,
file='R2_NMRFAM',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='ssNOE_NMRFAM',ri_type='NOE',frq=799.642*1e6,
file='ssNOE_NMRFAM',res_num_col=1,data_col=2,error_col=3)
interatom.define(spin_id1='@N',spin_id2='@H', direct_bond=True)
interatom.define(spin_id1='@NE1',spin_id2='@HE1',
direct_bond=True)
interatom.set_dist(spin_id1='@N*',spin_id2='@H*',ave_dist=1.
02*1e-10)
interatom.unit_vectors()
value.set(-172*1e-6,'csa',spin_id='@N*')
dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di
ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCA
L_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_num
=MC_NUM,conv_loop=CONV_LOOP)
So it indicates that my script has loaded. However, after it
loads the spins from the pdb file, this is what happens after my
first data
set has been loaded:
relax> relax_data.read(ri_id='R1_Agnes', ri_type='R1',
frq=599642000.0, file='R1_Agnes', dir=None, spin_id_col=None,
mol_name_col=None, res_num_col=1, res_name_col=None,
spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None,
spin_id=None)
Opening the file 'R1_Agnes' for reading.
RelaxWarning: The sequence data in the line ['Residue', 'R1',
'Error'] is invalid, the residue number data 'Residue' is invalid.
RelaxWarning: The sequence data in the line ['1'] is invalid, the
data is missing.
RelaxWarning: The sequence data in the line ['2'] is invalid, the
data is missing.
RelaxWarning: The sequence data in the line ['3'] is invalid, the
data is missing.
RelaxWarning: The sequence data in the line ['4'] is invalid, the
data is missing.
RelaxWarning: The sequence data in the line ['5'] is invalid, the
data is missing.
RelaxWarning: The sequence data in the line ['6'] is invalid, the
data is missing.
RelaxWarning: The sequence data in the line ['7'] is invalid, the
data is missing.
RelaxWarning: The sequence data in the line ['8'] is invalid, the
data is missing.
RelaxWarning: The sequence data in the line ['9'] is invalid, the
data is missing.
RelaxWarning: The sequence data in the line ['10'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['11'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['16'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['17'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['18'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['21'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['22'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['23'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['26'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['27'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['28'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['31'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['40'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['46'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['58'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['61'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['62'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['63'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['73'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['76'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['79'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['81'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['82'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['85'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['94'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['97'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['99'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['106'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['115'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['121'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['126'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['127'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['134'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['135'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['136'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['137'] is invalid,
the data is missing.
RelaxWarning: The sequence data in the line ['139'] is invalid,
the data is missing.
RelaxError: The spin ID '#hRGS7:12' corresponds to multiple
spins, including '#hRGS7:12@N' and '#hRGS7:12@H'.
crowlab: [~/relax-4.0.2]>
As you can see, I have all 6 data sets set to load, but only the
very first one appears to do so, and after it loads, it just exits
out of
relax. Again, I don't know if this is a problem with how I wrote
the
script. The Relax_script1 is the one that I load up to run the
whole thing.
The model free script.py is just the script it reads once relax
has opened
up. Again, I can see all the spins are properly loaded, and the
isotopes
are set. It just everything after the first data set that doesn't
load.
Thanks again in advance.
Sincerely,
Sam
On Thu, Sep 8, 2016 at 10:15 AM, Mahdi, Sam <
sam.mahdi.846@xxxxxxxxxxx> wrote:
Hi Troels,
Thank you so much. If there is any extra info you need please
let me know.
Sincerely,
Sam
On Thu, Sep 8, 2016 at 9:12 AM, Troels Emtekær Linnet <
tlinnet@xxxxxxxxxxxxx> wrote:
Hi Sam.
I will have some time on Tuesday, and then I will look at it.
Best
Troels
Den onsdag den 7. september 2016 skrev Mahdi, Sam <
sam.mahdi.846@xxxxxxxxxxx>:
Hello Troels,
I uploaded all the files, and even added in the entire output
that i recieved using model free in script mode. I didn't know
if all the
files uploaded need to have that link, so only the initial
files that were
uploaded it, have it.
Thank you in advance for your help!
Sincerely,
Sam
On Wed, Sep 7, 2016 at 12:41 AM, Troels Emtekær Linnet <
tlinnet@xxxxxxxxxxxxx> wrote:
Hi Sam.
You should be able to upload more files after the initial
upload.
In the comment thread, please also make a link to this
discussion.
https://mail.gna.org/public/relax-users/2016-09/threads.html
#00001
Best
Troels
2016-09-06 19:10 GMT+02:00 Mahdi, Sam <
sam.mahdi.846@xxxxxxxxxxx>:
Thank you for your reply. When I come to upload my data
though, I see there are only 4 available slots I can upload
my data. I have
a total of 6 data files however, that need to be uploaded (3
of each
frequency). I also need to upload the relax -i of 2 different
computers,
and the script file I've been using for a total of 9 files
that need to be
uploaded. Is there a way to increase the amount I can upload,
or can I
upload more after the initial submission?
On Mon, Sep 5, 2016 at 2:46 AM, Troels Emtekær Linnet <
tlinnet@xxxxxxxxxxxxx> wrote:
Hi Sam.
To solve this problem, it would be easier to have access to
some of your data.
Can you upload to: https://gna.org/bugs/?group=relax
Take each of your data files, and delete all data, except 2
spins.
Also provide your script file, or a description of which
button you press in the GUI.
Please also provide information about your system with:
relax -i
Then I will make a tutorial for you. To be added here:
http://wiki.nmr-relax.com/Category:Tutorials
If there is a problem in relax, I will write a systemtest
which will solve the problem.
And the problem will never return.
If this a user error, the tutorial should help to prevent
this, and would be the first step before
adding/modifying the manual.
Regarding using mpirun.
Have a look at this page. Maybe it helps.
http://wiki.nmr-relax.com/OpenMPI
Cheers.
2016-09-03 4:13 GMT+02:00 Mahdi, Sam <
sam.mahdi.846@xxxxxxxxxxx>:
Hello everyone,
So I was able to set up and run the dauvergne_protocol
successfully by
using the script in the wiki. The problem I have come
across now is the
program doesn't seem to read my data. Using the gui
interface I was able to
successfully load my data and run it. When I upload my
data using the
script command:
relax_data.read(ri_id='R1_Agne
s',ri_type='R1',frq=599.642*1e6,
file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
The output file simply gives errors for amino acids I
don't have data for:
RelaxWarning: The sequence data in the line ['1'] is
invalid, the data is
missing.
This is fine as relax just ignores these values and
continues its
calculations. I only receive this warning for values I
don't have data for.
This is the same thing I got when using the gui interface
(the gui however
showed my values that I have data for and the residue it
corresponds to,
using the script I don't receive such an output, I don't
know whether this
is normal or not). However, since I don't get this warning
for every amino
acid, I assume this means it has read the values for the
other amino acids.
All of my data is the same, relax warnings only pop up for
amino acids that
I don't have data for. The problem is, when I enter the
dAuvergne protocol,
I get the protocol working, it starts running local_tm
however it appears
none of my data has been uploaded:
RelaxWarning: The spin '#hRGS7:2@N' has been deselected
because of missing
relaxation data
RelaxWarning: The spin '#hRGS7:3@N' has been deselected
because of missing
relaxation data
And I get that warning for every single amino acid. From
the output, it
appears to have read the file since it knows exactly which
amino acids I
don't have data for, but I don't know why when it comes to
running the
protocol, it tells me I havn't inputed any data. I have
typed everything
directly according to the script from the wiki. From
running the protoco,
it appears everything has properly been uploaded,
structure data, magnetic
dipole interactions, csa, the data pipe, the analysis
variables, the python
module imports, and setting up the spins from the pdb
file. It appears the
only error is from loading the actual relaxation data.
On a completely unrelated side note, I have been
attempting to run relax on
multiple processors. I have tried 2 different computers,
both fedora linux.
I have mpi4py and openmpi downloaded on both. On one, I
can get relax on
multiple cores working (havn't been able to successfully
run it due to
being unable to upload any data properly). On the other
however, I type in
the mpirun -np --multi='mpi4py' script, but I get no
output. I can see that
it's running in the background (top command), but nothing
pops up, no text
command, nothing. I typed the same mpirun with the --gui,
but that opened
up nothing. On a uni-processor (typing in the exact same
command without
indicating how many cores i.e. no -np --multi='mpi4py') it
works just fine,
so I don't think its my openmpi that's an issue. I don't
know whether this
is an issue with my mpi4py or a personal computer issue
(since on the other
computer relax runs just fine on multiple cores).
Sincerely,
Sam
P.S. when I do enter the top command to see what's
running. My master shows
mpirun, and the 3 slaves display python when I put -np 4,
so I know
something is running in the background. I have 8 cores.
On Wed, Aug 31, 2016 at 6:49 PM, Mahdi, Sam <
sam.mahdi.846@xxxxxxxxxxx>
wrote:
Hello everyone,
I am attempting to run relax on a multi-processor mode.
I have been able
to successfully set-up relax to operate in a
multi-processor mode by using
the mpirun -np #ofprocessors /location/of/relax
--multi='mpi4py'
The problem I encounter is when using the --tee log
dauvergne_protocol.py
command. I receive this error
RelaxError: the script file 'dauvergne_protocol.py' does
not exist
I located the script file and tried to direct to it's
path
mpirun /usr/local/Relax/relax-2.2.5/relax
--multi='mpi4py' --tee log
/usr/local/Relax/relax-2.2.5/a
uto-analyses/dauvergne_protocol.py
But i received this error
RelaxError: the script file
'/usr/local/Relax/relax-2.2.5/
auto-analyses/dauvergne_protocol.py' does not exist.
Even though I have the script, it doesn't seem to be
able to locate it.
On a side note, in the manual, one dash doesn't actually
run the command.
I.e. in the manual it displays -multi='mpi4py' . What it
should be is
--multi='mpi4py' . The same goes for -tee. It should be
--tee.
Sincerely,
Sam
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Re: Using multi-processor for model_free