Re: Is it possible to analyse CPMG experiments with relax?

. Are there any others developing on this branch? Best Troels -- Troels Emtekær Linnet PhD student Copenhagen University SBiNLab, 3-0-41 Ole Maaloes Vej 5 2200 Copenhagen N Tlf: +45 353-22083 2013/5/2 Edward d'Auvergne edw...@nmr-relax.com Hi Troels, Welcome to the relax mailing lists. For now

Building relax from source using scons and a different python interpretor

minfx import readline import wx import numpy import scipy Best Troels Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org

Re: Building relax from source using scons and a different python interpretor

-rh5-x86_64/bin/python2.7 import relax relax.start(profile_flag=False) Best Troels Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 2013/5/2 Edward d'Auvergne edw...@nmr-relax.com Hi Troels, In the future, for such questions I would recommend asking

Necessary field separation for model-free calculation in nmr-relax

combination to solve the double minimum problem. But I wonder if this could be solved also for a 750/800 MHz data acquisition? Best Troels Emtekær Linnet ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org

Re: Custom Peak intensity reading

in the line ['protein', '75', 'L', '75', 'N', '3.578841e+06', '6.352595e+06'] is invalid, the data is missing. RelaxError: No corresponding data could be found within the file. --- Troels Emtekær Linnet 2013/6/6 Edward d'Auvergne edw...@nmr-relax.com: Hi, Have you had any

Re: Custom Peak intensity reading

I think it is because that: spectrum_id='(2,6)' is translated to a string. Could it be corrected, so it does similar as: int_col=(6, 7) Best Troels Emtekær Linnet 2013/6/6 Troels Emtekær Linnet tlin...@gmail.com: Hi, No, not any luck. And, this time I am not renaming. Where can I find

Re: Custom Peak intensity reading

developer you could give this a go yourself after creating the report. This would all go into the relax trunk, and then be ported to the relax_disp branch using svnmerge.py. Cheers, Edward On 6 June 2013 15:04, Troels Emtekær Linnet tlin...@gmail.com wrote: I think it is because

Is there a command for opening an auto analysis for a pipe?

I can do it by: Ctrl+D Right click, Associate with a new auto analysis Is there a relax command to open this? best Troels Emtekær Linnet ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe

Re: Is there a command for opening an auto analysis for a pipe?

-analysis is not needed at all. This just requires a few user function calls on a data pipe, set to maybe 'relax_fit', to trigger the issue. I hope this answers your question. Regards, Edward On 6 June 2013 18:48, Troels Emtekær Linnet tlin...@gmail.com wrote: I can do it by: Ctrl+D

Re: Time of running, Model selection and global/cluster analysis for relaxation dispersion analysis

14 2.41391 10.41391 ... But what if you run relax without the flag: -l LOGFILE.txt ??? Does the cdp class contain the information? Best Troels Best Troels Troels Emtekær Linnet 2013/6/11 Edward d'Auvergne edw...@nmr-relax.com Hi, I'll answer below

Re: Running with more that 1/2 CPU's

analysis create 4/5 different pipes for each fitting model. Would relax be able to handle 500 pipes? Here I worry about the final_state file, saving, and memory management. Is the memory released meanwhile? Or should I flush/delete the pipes/memory for each 1/100 run? Best Troels Troels Emtekær Linnet

Using | nmrPipe -fn REV \ for processing CPMG dispersiong experiments

. According to the manual: http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/rev.html The recommendation is to do a negative Fourier Transform | nmrPipe -fn FT -neg \ Is there a special reason for | nmrPipe -fn REV \ Best Troels Emtekær Linnet ___ relax

Running scripts inside relax

Emtekær Linnet ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org

Re: Running scripts inside relax

If I run: relax_disp relax_1_ini.py relax runs through the script and exit. Is there a way to stop after reading? Best Troels Emtekær Linnet 2013/8/26 Edward d'Auvergne edw...@nmr-relax.com: Hi Troels, You should find the answer you are after in the following link: http://www.nmr

Fwd: Made a wiki page for a Tutorial for Relaxation dispersion analysis cpmg fixed time recorded on varian as fid interleaved

students in our lab, who can have a little trouble handling linux. It therefore contains some helper scripts, to help processing spectra. Any comments would be appreciated. :-) Troels Emtekær Linnet ___ relax (http://www.nmr-relax.com) This is the relax

Re: Made a wiki page for a Tutorial for Relaxation dispersion analysis cpmg fixed time recorded on varian as fid interleaved

All-right. I will de-couple scripts. :-) For images: http://en.wikipedia.org/wiki/Wikipedia:Picture_tutorial Troels Emtekær Linnet 2013/8/27 Edward d'Auvergne edw...@nmr-relax.com: Hi Troels, For this relaxation dispersion tutorial for relax, I would suggest including the contents

Re: Made a wiki page for a Tutorial for Relaxation dispersion analysis cpmg fixed time recorded on varian as fid interleaved

Now corrected. :-) Is it better now? :-) Troels Emtekær Linnet 2013/8/27 Troels Emtekær Linnet tlin...@gmail.com: All-right. I will de-couple scripts. :-) For images: http://en.wikipedia.org/wiki/Wikipedia:Picture_tutorial Troels Emtekær Linnet 2013/8/27 Edward d'Auvergne edw

Re: Peak list reading

Hi Min-Kyu. I believe you probably need to define the right header for the file. ex: Assignment w1 w2 Data Height And see if you can fix the question marks. 568N-HN Have a look in the test-suite for some typical definition of peaks files.

Re: Most efficient way to compare spin.X values between pipes

GMT+01:00 Troels Emtekær Linnet tlin...@nmr-relax.com: Hi, I need an efficient way to compare spin.X values between pipes. Here X could be: - spin.r2eff - spin.chi2 - spin.kex etc. I have tried implementing the following: for spin, mol_name, res_num, res_name, spin_id in spin_loop

Re: Installation of relax under Mac OS

Hi Mengjun. If you have Mavericks and are in for trying to compile yourself, then try this guide I have written: http://wiki.nmr-relax.com/Installation_mac_mavericks_os_x If you are experienced linux user, and want to use scripts for dataanalysis, this should be the best way. Let me know if you

Re: Installation of relax under Mac OS

, Mengjun Quoting Troels Emtekær Linnet tlin...@nmr-relax.com: Hi Mengjun. If you have Mavericks and are in for trying to compile yourself, then try this guide I have written: http://wiki.nmr-relax.com/Installation_mac_mavericks_os_x If you are experienced linux user, and want to use

Re: unexpected mf S2 values

Dear Soumya. Would you be able to provide the script you have used for the analysis? Or did you use the GUI? That could help find possible errors. I guess that it would be something similar to: http://www.nmr-relax.com/manual/Single_model_free_model_script_mode_sample_script.html If you have

Re: Relaxation curve fitting

Dear Mengjun. For xmgrace installation, follow this: http://wiki.nmr-relax.com/Installation_windows_Python_x86-32_Visual_Studio_Express_for_Windows_Desktop#xmgrace_-_for_the_plotting_results_of_NMR-relax In short. 1 ) Download and install 2) Copy qtgrace.exe to xmgrace.exe in same folder 3) Add

Re: Relaxation curve fitting

these files to plot in any program. Or use the User function: Grace write, to make grace files. Best Troels 2014-03-03 16:33 GMT+01:00 Troels Emtekær Linnet tlin...@nmr-relax.com: Dear Mengjun. For xmgrace installation, follow this: http://wiki.nmr-relax.com/Installation_windows_Python_x86

Re: error message

Hi Stefano. Which version of relax are you using? If relax is an older version, the isotope function is not introduced You can try: relax -v relax -i If relax is newer, then you probably have forgotten to tell which isotope you are investigating. N15 ? In the prompt, you need this:

Re: tests

Hi Stegano. Can you run: relax -s --time -t systemtest.txt That will run the systemtest, adding time information, and both tee to screen and to logfile systemtest.txt Then we should be able to figure out which systemtest is failing. 2014-03-14 17:42 GMT+01:00 Stefano Luciano Ciurli

Re: error message

, I will send it to you. Thanks, Stefano On Mar 14, 2014, at 5:31 PM, Troels Emtekær Linnet wrote: Hi Stefano. Which version of relax are you using? If relax is an older version, the isotope function is not introduced You can try: relax -v relax -i If relax is newer, then you probably

Re: error message

Hi Stefano. You have the mac app relax 3.5 installed ? Then relax is only reached in the GUI i think. :-) Those commands would be: Tools - System information Best Troels 2014-03-17 10:33 GMT+01:00 Stefano Luciano Ciurli stefano.ciu...@unibo.it: Hi Troels, You can try: relax -v relax

Re: tests

Hi Stefano. You have the mac app relax 3.5 installed ? Then relax is only reached in the GUI i think. :-) To run the systemtests, then do: Tools - System tests Copy paste the info from the output of the relax controller to a file. When relax hits an error, it will show which test is wrong, and

Re: Error message upon PDB loading

Dear Stefano. You are really not bugging anyone with your questions! It is a welcome to see the interest in relax, and if you are becoming interested and a power user, the knowledge of relax is spread. :-) But for being able to help you, please dont hesitate to make a bug report.

Re: numeric values of d and c

Or open the relax prompt Ctrl+p And write: script(script.py) OUT COME - script = 'script.py' # Python module imports. from numpy import float64, zeros # relax module

Re: ref/set intensity plots don't get written

Hi Justin. I guess that you trying to plot a parameter as function of residue number. I guess that something is wrong with: y_data_type='ref' or y_data_type='sat' If you go into the spin viewer, and select a spin, you should be able to find the parameter which you can plot? Best Troels

Re: Model-free analysis error

Hi Ivanhoe. I remember that Edward added a section to the manual about running time, and probably somewhere on the relax mailing list that question is answered. But it depends on how many spins, computer power, and how many CPU. But I think that anything between a day and a week is expected

Re: R2 from R1rho R1

Dear Justin. If you have R1 values measured from an experiment. And you have R1rho intensities measured as variations of spin-lock time, spin-lock offset and spin-lock field/power, you can perform R1rho analysis in relax. If we just think of model DPL94, you would in relax get fitted R20(or

Re: R1rho RD analysis

Hi Peixiang. For model selection, try this in relax. The help section is the best you can get ! Just start relax in terminal: relax Then write: relax help(relax_disp) to see all options. For example: help(relax_disp.select_model) You can find more info at the wiki:

Re: R1rho RD analysis

If you find this helpful, you could maybe continue this R1rho tutorial at the wiki? I wrote the tutorial, because I know the learning curve is steep. And it have helped our students in the lab since. Best Troels 2014-05-22 17:13 GMT+02:00 Troels Emtekær Linnet tlin...@nmr-relax.com: Hi Peixiang

Re: R1rho RD analysis

Dear Peixiang, Dear Andrew. Just a little heads-up. Within a week or two, we should be able to release a new version of relax. This update has focused on speed, recasting the data to higher dimensional numpy arrays, and moving the multiple dot operations out of the for loops. So we have quite

Re: R1rho RD analysis

. On 26/06/2014 09:00, Troels Emtekær Linnet wrote: Dear Peixiang, Dear Andrew. Just a little heads-up. Within a week or two, we should be able to release a new version of relax. This update has focused on speed, recasting the data to higher dimensional numpy arrays, and moving

Re: R1rho RD analysis

then you can get some speedups. But in my hands at least, those algorithms only tend to work well on huge matrices that are really sparse (eg100x100 with not much over 10% of elements having entries). On 26/06/2014 09:44, Troels Emtekær Linnet wrote: Hi Andrew. I am looking for a solution

Re: Relax - model free without a structure/PDB?

. - The relax manual can be expanded, to help future users in same situation. Good luck! Best Troels Emtekær Linnet PhD student Copenhagen University SBiNLab, 3-0-41 Ole Maaloes Vej 5 2200 Copenhagen N Tlf: +45 353-22083 Lync Tlf: +45 353-30195 2014-07-31 21:47 GMT+02:00 Ryan Lo rhl

Re: field strength off-resonance R1rho constant relax time relaxation dispersion

relax_disp.spin_lock_field(spectrum_id=sp_id, field=spin_lock_field_strength) I hope this helps! Please write back here to the mailing list, if the answer covers your question. Good luck! Best Troels Emtekær Linnet PhD student Copenhagen University SBiNLab, 3-0-41 Ole Maaloes Vej 5 2200 Copenhagen N Tlf: +45 353

Re: R1rho RD analysis

Dear Peixiang. I have just discovered a bug in relax, where the 'relax_times' is not properly loaded from the data-store and sent to the target function of model NS R1rho 2-site. This means that currently 'NS R1rho 2-site' can only be used for fixed time at the moment. This bug has no influence

Re: field strength off-resonance R1rho constant relax time relaxation dispersion

, to help future users in same situation. Good luck! Best Troels Emtekær Linnet PhD student Copenhagen University SBiNLab, 3-0-41 Ole Maaloes Vej 5 2200 Copenhagen N Tlf: +45 353-22083 Lync Tlf: +45 353-30195 2014-08-20 18:56 GMT+02:00 Atul Srivastava asriv...@umn.edu: Dear Edward, I already

Re: field strength off-resonance R1rho constant relax time relaxation dispersion

, Troels Emtekær Linnet tlin...@nmr-relax.com wrote: [snip] relax_disp.relax_time(spectrum_id=id, time=relax_time) - This is used for the initial R2eff calculation, for exponential curve fitting. # Set the NMR field strength of the spectrum. spectrometer.frequency(id=id, frq=H_frq

Is there a way to clear the Monte Carlo simulation data key?

Dear Edward. Is there a way to clear the Monte Carlo simulation data key? I try to run some data with increasing number of Monte Carlo simulations. Thank you. Best Troels ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list

Re: Is there a way to clear the Monte Carlo simulation data key?

, and this is preserved in the Monte Carlo simulation structures as well. Regards, Edward On 28 August 2014 11:14, Troels Emtekær Linnet tlin...@nmr-relax.com wrote: Dear Edward. Is there a way to clear the Monte Carlo simulation data key? I try to run some data with increasing number of Monte

Re: Relaxation dispersion clustering calculation time

of conformational exchange properties. Troels Emtekær Linnet PhD student Copenhagen University SBiNLab, 3-0-41 2014-09-09 9:48 GMT+02:00 Edward d'Auvergne edw...@nmr-relax.com: Hi Chung-ke, Welcome to the relax mailing lists! Thanks to the hard work of one of the relax developers - Troels Linnet

Re: Relaxation dispersion clustering calculation time

:00 Troels Emtekær Linnet tlin...@nmr-relax.com: Hi Chung-ke. Can you put the information about which version of relax you use? You can in terminal do: relax -i and write it here. And then there is the question if you used data from one field or two spectrometer fields. Fitting to one

Re: Relaxation dispersion clustering calculation time

and R20b numbers are really funky. I shall follow your suggestions and run the calculations with the CR72 and B14 models instead. Cheers, Chung-ke On Sep 9, 2014, at 4:25 PM, Troels Emtekær Linnet tlin...@nmr-relax.com wrote: Hi Chung-ke. Can you put the information about which version

How does the error intensity analysis handle both specification of baseplane RMSD and partly repeated spectrum?

Dear Edward. I was wondering how relax handles the error intensity analysis, where one both specify the baseplane RMSD and and one also have partly repeated spectrums? For example you have recorded for 10 time series. You measure the baseplane RMSD for each spectrum. You have repeated

Re: C modules not compiled

Hi. Try just write scons But this should only be for the source code. The packaged versions should already have the compiled C code in it. So this is weird. Can you run relax - d and post it here? Best Troels On 13 Nov 2014 22:34, Maciejewski,Mark W. ma...@uchc.edu wrote: Hello, I have

Re: error while running relax-GUI tutorial

point before staring the analysis. Best Troels 2014-11-18 11:51 GMT+01:00 Troels Emtekær Linnet tlin...@nmr-relax.com: Dear Prem. Welcome to the mailing list! I guess that you mean the manual at: http://www.nmr-relax.com/manual/Contents.html The relaxation dispersion auto-analysis

Re: If I can run modelfree analysis using relaxation data from only single magnetic field?

Hi Danyun Zeng. Try have a look on this wiki page: http://wiki.nmr-relax.com/Model-free_analysis_single_field Best Troels 2015-01-28 1:13 GMT+01:00 Danyun Zeng zeng...@hotmail.com: Hi, all, I'm new to relax. I want to use it for modelfree analysis recently and I only have a set of

Re: Error calculation of individual parameter dw from MC

, 3.6397883716309427]) print len(a) print np.std(a, ddof=1) --- 500 0.105036572661 --- But the error in relax is: cdp.mol[0].res[81].spin[0].dw_err 0.046827775338478594 Is there something I am missing here? Best Troels Troels Emtekær Linnet 2015-01-14 13:05 GMT+01:00 Troels Emtekær

Re: Error calculation of individual parameter dw from MC

. I note the same behaviour for r2. Best Troels Troels Emtekær Linnet 2015-01-14 13:20 GMT+01:00 Troels Emtekær Linnet tlin...@gmail.com: If I isolate the sim dw cdp.mol[0].res[81].spin[0].dw_sim Copy output from prompt to small test.py file. --- import numpy as np

Error calculation of individual parameter dw from MC

fittings. Would this be wrong? Best Troels Troels Emtekær Linnet ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options

Re: Help with setting up relax files

Hi Sam. Try to have a look on the wiki: http://wiki.nmr-relax.com/Category:Tutorials http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved Maybe you can figure out something. If you need more help. Make a suppert request

Re: fixed tm values

Dear Christina Möller. I am sure Edward can give you an answer to this. I know that he is on holiday until the 7th, so he will probably first respond after this. Until then, I can try to give you some temporary idea's you can work with. Beforehand, I would like to say, that I no experience with

Re: using relax on supercomputer

Dear Lora. I am interested in achieving the same thing on our small local computer cluster. I have read from http://beagle.ci.uchicago.edu/using-beagle/ That you use Torque to submit jobs. Have you succeeded in getting this to work with relax? Best Troels 2015-05-15 19:52 GMT+02:00 Lora

Re: using relax on supercomputer

. Thanks again! Best Troels 2015-05-29 11:46 GMT+02:00 Troels Emtekær Linnet tlin...@nmr-relax.com: Dear Lora. I am interested in achieving the same thing on our small local computer cluster. I have read from http://beagle.ci.uchicago.edu/using-beagle/ That you use Torque to submit jobs

Experimental: Try relax at Google Cloud Computing

Hi relax users. I have written a tutorial to get relax running at Google Cloud Computing. The tutorial can be found here: http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computing Consider this as a very experimental procedure. The Cost of running Google Cloud Computing has been rapidly

Re: model free analysis: spin deselection problem

Hi. My colleagues Kresten Lindorff-Larsen and Amelie Stein kindly helped me find some references: http://zhanglab.ccmb.med.umich.edu/HAAD/ http://zhanglab.ccmb.med.umich.edu/papers/2009_7.pdf Fortran code: http://zhanglab.ccmb.med.umich.edu/HAAD/haad.f90

Re: Data files

Hi Rakes. Look in the test_suite folder. Hundreds of unit and system test is provided there. Best Troels 2016-05-27 14:21 GMT+02:00 Rakesh Sharma : > Hi everyone, > can anybody have idea that from where to get data files used in relax > manual calculations. I am

Re: Spectral data corresponding to the ID string xxx does not exist

Hi Karin. Can you provide the header or say 10 first lines of one of the files? Is the above the list of files used for the experiment? Best Troels 2016-03-25 0:47 GMT+01:00 Crowhurst, Karin A : > Hello, > > > I am new to Relax and have been trying to setup my R1

Re: Issue in ModelFree Calculation

Hi. Did you compile relax yourself? Try compiled version of relax. Have you tried running the systemtests? http://wiki.nmr-relax.com/Installation_test It looks like you are running mpirun. Try running without. Or look here: http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computing

Re: Error in model free analysis

Hi Ashish. Attachments to the mailserver is dropped. Can you provide a bug report instead, at upload the file there? https://gna.org/bugs/?func=additem=relax Best Troels 2017-02-22 8:56 GMT+01:00 Ashish Sethi : > Dear Edward, > > > > I also tried running the same

Re: Using multi-processor for model_free

ree 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 < > tlin..

Re: Using multi-processor for model_free

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 th

Re: Using multi-processor for model_free

form. I can send the screenshots and the relax -i for both > computers again. I don't know why it doesn't work the fedora 24. Do you > know what could be causing this? > > Thanks again in advance > > On Tue, Sep 13, 2016 at 9:32 PM, Troels Emtekær Linnet < > tlin.

Re: Using multi-processor for model_free

n specified. >> >> Sincerely, >> Sam >> >> On Mon, Sep 26, 2016 at 2:19 PM, Mahdi, Sam <sam.mahdi@my.csun.edu> >> wrote: >> >>> Hi Troels, >>> >>> I have attempted the fix for running on a multi-processor platform by >>> creatin

Re: Using multi-processor for model_free

;>> >>> I have attempted the fix for running on a multi-processor platform by >>> creating the script you told me too, and I still got the same result. I >>> have uploaded a screenshot that shows again, relax is running in the >>> background, but there is

Re: Using multi-processor for model_free

To test the speed difference between script and GUI, you could try to run the full test-suite through the terminal or inside the GUI. That should give you a clue about time difference. 2016-09-28 20:32 GMT+02:00 Troels Emtekær Linnet <tlin...@nmr-relax.com>: > If you get differen

Re: Using multi-processor for model_free

ordinate set has not been specified >> By removing the extra N, all the text for the 3D location (the >> co-ordinates) for the HN were shifted a space (no longer aligned). Once I >> aligned them all, relax was able to read all the spins. So its working now. >> I'm currently run

Re: Using multi-processor for model_free

2:43 PM, Troels Emtekær Linnet < > tlin...@nmr-relax.com > <javascript:_e(%7B%7D,'cvml','tlin...@nmr-relax.com');>> wrote: > >> Hi Sam. >> >> Akk you PI to run this: >> >> sudo -- sh -c 'setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc; pip >>

Re: Using multi-processor for model_free

--report-bindings -np 2 python --version > Python 2.7.5 > Python 2.7.5 > > crowlab: [~]> > crowlab: [~]> echo "> mpirun --report-bindings -np 2 /usr/bin/env python > --version"; mpirun --report-bindings -np 2 /usr/bin/env python --version; > echo ""

Re: Using multi-processor for model_free

i info. I already have minfx 1.0.12 with > 4.0.2. But I can't open relax on multi processor platform for either > version. > > On Mon, Sep 19, 2016 at 10:47 AM, Troels Emtekær Linnet < > tlin...@nmr-relax.com> wrote: > >> Please upgrade! >> >> Name

Re: Using multi-processor for model_free

grid_search > model_lower, model_upper, model_inc = grid_setup(lower, upper, inc, > verbosity=verbosity, skip_preset=skip_preset) > File "/home/sam2/relax-4.0.2/pipe_control/minimise.py", line 341, in > grid_setup > elif values[i] in [None, {}, []]: > IndexErro

Re: Using multi-processor for model_free

that wouldn't change any of the calculations > correct? I never have since I assumed relax would just ignore all the amino > acids I don't have data for, but it may help increase the speed of my > calculations if I just tell relax to just ignore the spins from the start. > > Sincerel

Re: Using multi-processor for model_free

s >> correct? I never have since I assumed relax would just ignore all the amino >> acids I don't have data for, but it may help increase the speed of my >> calculations if I just tell relax to just ignore the spins from the start. >> >> Sincerely, >> Sam >

Re: Using multi-processor for model_free

On Tue, Sep 20, 2016 at 9:15 AM, Troels Emtekær Linnet < > tlin...@nmr-relax.com> wrote: > >> Hi Sam. >> >> On >> https://gna.org/bugs/?25084 >> >> I cannot open the file.? >> >> In the meantime, try to specify the full path to relax. Not

Re: Using multi-processor for model_free

nd 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 < > tlin...@nmr-relax.

Re: Using multi-processor for model_free

Hi Troels, >>> >>> I have attempted the fix for running on a multi-processor platform by >>> creating the script you told me too, and I still got the same result. I >>> have uploaded a screenshot that shows again, relax is running in the >>> background, but ther

Re: Using multi-processor for model_free

Sam. All points to: "./relax" is NOT calling relax in the current folder. It is because the command "mpirun" is running it. Please provide the FULL path to relax. I think I have written this before. ;) Best Troels 2016-09-30 19:24 GMT+02:00 Mahdi, Sam : >

Re: Using multi-processor for model_free

1. Mpi4py 2.0.0 process 1 of 2 on instance-1. [tlinnet@instance-1 ~]$ mpirun --np 2 relax_4.0.2 --multi='mpi4py' --version relax 4.0.2 2016-10-03 12:39 GMT+02:00 Troels Emtekær Linnet <tlin...@nmr-relax.com>: > Hi Sam. > > The commands reflect the BASH shell and not TCSH. > Thats w

Re: Using multi-processor for model_free

ion of > relax (the other one I have is 2.2.5) and the older version of openmpi, and > attempt to run it then? It would be a lot easier for me to directly tell my > PI to simply remove a file, or update one, then to attempt to troubleshoot > with them. > > Sincerely, > Sam

Re: Using multi-processor for model_free

> Hi Troels, > > I attempted the full path > mpirun -np 5 ~/relax-4.0.2/relax --multi="mpi4py" -v > and still got the same result. No output. > > Sincerely, > Sam > > On Fri, Sep 30, 2016 at 11:43 AM, Troels Emtekær Linnet < > tlin...@nmr-relax.com> w

Re: Using multi-processor for model_free

du>: > I get the same results with the full path mpirun -np 5 ~/relax-4.0.2/relax > --multi="mpi4py" -v > Still no output. > > Sincerely, > Sam > > On Fri, Sep 30, 2016 at 10:39 AM, Troels Emtekær Linnet < > tlin...@nmr-relax.com> wrote: > &g

Re: Using multi-processor for model_free

e know! > > Sincerely, > Sam > > > On Fri, Sep 30, 2016 at 2:23 PM, Troels Emtekær Linnet < > tlin...@nmr-relax.com> wrote: > >> Hi Sam. >> >> I am trying to setup myself on Google Cloud Platform. >> >> Here I setting up for a Redhat 6 dis

Re: Using multi-processor for model_free

-01 0:22 GMT+02:00 Troels Emtekær Linnet <tlin...@nmr-relax.com>: > Hi Sam. > > Can you try: > mpirun --version > > Thanks > > 2016-10-01 0:00 GMT+02:00 Mahdi, Sam <sam.mahdi@my.csun.edu>: > >> Hi Troels, >> >> Here is a list of the

Re: Using multi-processor for model_free

, but there is no output for relax, nor can I input any commands. > The only output I recieve is this: > Running relax with NP=$NPROC+8|bc in multi-processor mode > > And any command I type in after that gets no response. > > Sincerely, > Sam > > > On Sun, Sep 25,

Re: Using multi-processor for model_free

16 at 1:30 PM, Mahdi, Sam <sam.mahdi@my.csun.edu> >> wrote: >> >>> Hi Troels, >>> >>> An update on protein number 1: I have successfully resolved the problem. >>> Initially the pdb file had HN instead of just H for the backbone hydrogens. >>

Re: Using multi-processor for model_free

t = "crowlab: [%c]> "' > alias cwdcmd 'setprompt' > setprompt >endif > > Also, the 2nd command gave me no responce. > crowlab: [~]> alias get 'set noglob; wget http://svn.gna.org/viewcvs/* > checkout*/relax/trunk/devel_scripts/openmpi_test_install_

Re: 13C relaxation Model-free

Hi Sahil. Try the tutorials listed here: http://wiki.nmr-relax.com/Category:Tutorials http://wiki.nmr-relax.com/Tutorial_for_the_relaxation_dispersion_auto-analysis_in_the_GUI http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi http://wiki.nmr-relax.com/Manual I can get access