error on the diffusion tensor parameters
Hi all, I have a script to calculate errors on the diffusion tensor parameters, written by one of my former colleagues. It works well with relax v 3.2.3 however, in the version 3.3.3, it doesn't work and gives an error message saying ImportError: No module named my_relax.tensor_mc. I was wondering if the module has been renamed/replaced to something else or is this something entirely different. Thanks, Vineet Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ___ 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/listinfo/relax-users
AW: error on the diffusion tensor parameters
Dear Edward, Following is the error, Traceback (most recent call last): File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/processor.py, line 494, in run self.callback.init_master(self) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/__init__.py, line 318, in default_init_master self.master.run() File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/relax.py, line 199, in run self.interpreter.run(self.script_file) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 279, in run return run_script(intro=self.__intro_string, local=locals(), script_file=script_file, show_script=self.__show_script, raise_relax_error=self.__raise_relax_error) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 585, in run_script return console.interact(intro, local, script_file, show_script=show_script, raise_relax_error=raise_relax_error) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 484, in interact_script exec_script(script_file, local) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 363, in exec_script runpy.run_module(module, globals) File /opt/scisoft64/usr/lib/python2.7/runpy.py, line 180, in run_module fname, loader, pkg_name) File /opt/scisoft64/usr/lib/python2.7/runpy.py, line 72, in _run_code exec code in run_globals File /home/vpan014/NMR_900_FZJ_data/Relax/Apo_structure1_09122014/run17_structure/relax_mc_difftensor_print_all.py, line 11, in module from my_relax.tensor_mc import Main, print_fancy, Out_tensor ImportError: No module named my_relax.tensor_mc I am checking with my former labmate who wrote the script regarding the module as well. I also had a question regarding possibility of performing Monte Carlo simulations to get errors on the model free parameters within all the four diffusion tensor models. I mean, normally, the MC simulations are performed once a particular diffusion tensor is selected using the AIC. Is there a way to do the simulations on rest of the tensor models as well? Cheers, Vineet Hi Vineet, Could you copy and paste the entire error? That would significantly help working out what is happening, as it will indicate where the error is happening. But if you search for the text my_relax or file my_relax.py, you will see that this has never existed in any version of relax, from 2001 until now. Regards, Edward ___ On 18 December 2014 at 15:09, Panwalkar, Vineet Hi all, I have a script to calculate errors on the diffusion tensor parameters, written by one of my former colleagues. It works well with relax v 3.2.3 however, in the version 3.3.3, it doesn't work and gives an error message saying ImportError: No module named my_relax.tensor_mc. I was wondering if the module has been renamed/replaced to something else or is this something entirely different. Thanks, Vineet ___ 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/listinfo/relax-users Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ___ 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/listinfo/relax-users
Re: error on the diffusion tensor parameters
Hi Vineet, From the error message, the my_relax module is clearly a special Python or relax module written by your former college. It is not part of relax, so I can't help you much. You might be able to find it on your system by typing: $ locate my_relax.py $ locate tensor_mc.py The missing external module will have one of these names. If it is tensor_mc.py, then this will be in the directory my_relax/. All the contents of that directory is then called a Python package, and you will need all of it. I hope this information helps. It is a pity your former college did not contribute it to relax so that I can help you more. Regards, Edward On 18 December 2014 at 15:36, Panwalkar, Vineet v.panwal...@fz-juelich.de wrote: Dear Edward, Following is the error, Traceback (most recent call last): File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/processor.py, line 494, in run self.callback.init_master(self) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/__init__.py, line 318, in default_init_master self.master.run() File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/relax.py, line 199, in run self.interpreter.run(self.script_file) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 279, in run return run_script(intro=self.__intro_string, local=locals(), script_file=script_file, show_script=self.__show_script, raise_relax_error=self.__raise_relax_error) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 585, in run_script return console.interact(intro, local, script_file, show_script=show_script, raise_relax_error=raise_relax_error) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 484, in interact_script exec_script(script_file, local) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 363, in exec_script runpy.run_module(module, globals) File /opt/scisoft64/usr/lib/python2.7/runpy.py, line 180, in run_module fname, loader, pkg_name) File /opt/scisoft64/usr/lib/python2.7/runpy.py, line 72, in _run_code exec code in run_globals File /home/vpan014/NMR_900_FZJ_data/Relax/Apo_structure1_09122014/run17_structure/relax_mc_difftensor_print_all.py, line 11, in module from my_relax.tensor_mc import Main, print_fancy, Out_tensor ImportError: No module named my_relax.tensor_mc I am checking with my former labmate who wrote the script regarding the module as well. I also had a question regarding possibility of performing Monte Carlo simulations to get errors on the model free parameters within all the four diffusion tensor models. I mean, normally, the MC simulations are performed once a particular diffusion tensor is selected using the AIC. Is there a way to do the simulations on rest of the tensor models as well? Cheers, Vineet Hi Vineet, Could you copy and paste the entire error? That would significantly help working out what is happening, as it will indicate where the error is happening. But if you search for the text my_relax or file my_relax.py, you will see that this has never existed in any version of relax, from 2001 until now. Regards, Edward ___ On 18 December 2014 at 15:09, Panwalkar, Vineet Hi all, I have a script to calculate errors on the diffusion tensor parameters, written by one of my former colleagues. It works well with relax v 3.2.3 however, in the version 3.3.3, it doesn't work and gives an error message saying ImportError: No module named my_relax.tensor_mc. I was wondering if the module has been renamed/replaced to something else or is this something entirely different. Thanks, Vineet ___ 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/listinfo/relax-users Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
AW: error on the diffusion tensor parameters
Hello Edward, Thanks for the reply. I am trying to get hold of all the missing modules. Once they are all at one place, I will put it into relax with his permission. I had another small query. I was wondering if there was a possibility to extract errors on the model free parameters within all the four diffusion tensor models. I mean, normally, the MC simulations are performed once a particular diffusion tensor is selected using the AIC. Is there a way to do the this on rest of the tensor models as well, either before the AIC selection or after it separately? Regards, Vineet An: Panwalkar, Vineet Cc: relax-users@gna.org Betreff: Re: error on the diffusion tensor parameters Hi Vineet, From the error message, the my_relax module is clearly a special Python or relax module written by your former college. It is not part of relax, so I can't help you much. You might be able to find it on your system by typing: $ locate my_relax.py $ locate tensor_mc.py The missing external module will have one of these names. If it is tensor_mc.py, then this will be in the directory my_relax/. All the contents of that directory is then called a Python package, and you will need all of it. I hope this information helps. It is a pity your former college did not contribute it to relax so that I can help you more. Regards, Edward On 18 December 2014 at 15:36, Panwalkar, Vineet v.panwal...@fz-juelich.de wrote: Dear Edward, Following is the error, Traceback (most recent call last): File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/processor.py, line 494, in run self.callback.init_master(self) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/__init__.py, line 318, in default_init_master self.master.run() File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/relax.py, line 199, in run self.interpreter.run(self.script_file) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 279, in run return run_script(intro=self.__intro_string, local=locals(), script_file=script_file, show_script=self.__show_script, raise_relax_error=self.__raise_relax_error) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 585, in run_script return console.interact(intro, local, script_file, show_script=show_script, raise_relax_error=raise_relax_error) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 484, in interact_script exec_script(script_file, local) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 363, in exec_script runpy.run_module(module, globals) File /opt/scisoft64/usr/lib/python2.7/runpy.py, line 180, in run_module fname, loader, pkg_name) File /opt/scisoft64/usr/lib/python2.7/runpy.py, line 72, in _run_code exec code in run_globals File /home/vpan014/NMR_900_FZJ_data/Relax/Apo_structure1_09122014/run17_structure/relax_mc_difftensor_print_all.py, line 11, in module from my_relax.tensor_mc import Main, print_fancy, Out_tensor ImportError: No module named my_relax.tensor_mc I am checking with my former labmate who wrote the script regarding the module as well. I also had a question regarding possibility of performing Monte Carlo simulations to get errors on the model free parameters within all the four diffusion tensor models. I mean, normally, the MC simulations are performed once a particular diffusion tensor is selected using the AIC. Is there a way to do the simulations on rest of the tensor models as well? Cheers, Vineet Hi Vineet, Could you copy and paste the entire error? That would significantly help working out what is happening, as it will indicate where the error is happening. But if you search for the text my_relax or file my_relax.py, you will see that this has never existed in any version of relax, from 2001 until now. Regards, Edward ___ On 18 December 2014 at 15:09, Panwalkar, Vineet Hi all, I have a script to calculate errors on the diffusion tensor parameters, written by one of my former colleagues. It works well with relax v 3.2.3 however, in the version 3.3.3, it doesn't work and gives an error message saying ImportError: No module named my_relax.tensor_mc. I was wondering if the module has been renamed/replaced to something else or is this something entirely different. Thanks, Vineet ___ 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/listinfo/relax-users
Re: error on the diffusion tensor parameters
Hi Vineet, After an analysis, anything is possible using the relax user functions. That includes performing Monte Carlo simulations on any model you wish. Have a look at some of the sample scripts for the sequence of user functions required. Regards, Edward On 18 December 2014 at 16:33, Panwalkar, Vineet v.panwal...@fz-juelich.de wrote: Hello Edward, Thanks for the reply. I am trying to get hold of all the missing modules. Once they are all at one place, I will put it into relax with his permission. I had another small query. I was wondering if there was a possibility to extract errors on the model free parameters within all the four diffusion tensor models. I mean, normally, the MC simulations are performed once a particular diffusion tensor is selected using the AIC. Is there a way to do the this on rest of the tensor models as well, either before the AIC selection or after it separately? Regards, Vineet An: Panwalkar, Vineet Cc: relax-users@gna.org Betreff: Re: error on the diffusion tensor parameters Hi Vineet, From the error message, the my_relax module is clearly a special Python or relax module written by your former college. It is not part of relax, so I can't help you much. You might be able to find it on your system by typing: $ locate my_relax.py $ locate tensor_mc.py The missing external module will have one of these names. If it is tensor_mc.py, then this will be in the directory my_relax/. All the contents of that directory is then called a Python package, and you will need all of it. I hope this information helps. It is a pity your former college did not contribute it to relax so that I can help you more. Regards, Edward On 18 December 2014 at 15:36, Panwalkar, Vineet v.panwal...@fz-juelich.de wrote: Dear Edward, Following is the error, Traceback (most recent call last): File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/processor.py, line 494, in run self.callback.init_master(self) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/__init__.py, line 318, in default_init_master self.master.run() File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/relax.py, line 199, in run self.interpreter.run(self.script_file) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 279, in run return run_script(intro=self.__intro_string, local=locals(), script_file=script_file, show_script=self.__show_script, raise_relax_error=self.__raise_relax_error) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 585, in run_script return console.interact(intro, local, script_file, show_script=show_script, raise_relax_error=raise_relax_error) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 484, in interact_script exec_script(script_file, local) File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, line 363, in exec_script runpy.run_module(module, globals) File /opt/scisoft64/usr/lib/python2.7/runpy.py, line 180, in run_module fname, loader, pkg_name) File /opt/scisoft64/usr/lib/python2.7/runpy.py, line 72, in _run_code exec code in run_globals File /home/vpan014/NMR_900_FZJ_data/Relax/Apo_structure1_09122014/run17_structure/relax_mc_difftensor_print_all.py, line 11, in module from my_relax.tensor_mc import Main, print_fancy, Out_tensor ImportError: No module named my_relax.tensor_mc I am checking with my former labmate who wrote the script regarding the module as well. I also had a question regarding possibility of performing Monte Carlo simulations to get errors on the model free parameters within all the four diffusion tensor models. I mean, normally, the MC simulations are performed once a particular diffusion tensor is selected using the AIC. Is there a way to do the simulations on rest of the tensor models as well? Cheers, Vineet Hi Vineet, Could you copy and paste the entire error? That would significantly help working out what is happening, as it will indicate where the error is happening. But if you search for the text my_relax or file my_relax.py, you will see that this has never existed in any version of relax, from 2001 until now. Regards, Edward ___ On 18 December 2014 at 15:09, Panwalkar, Vineet Hi all, I have a script to calculate errors on the diffusion tensor parameters, written by one of my former colleagues. It works well with relax v 3.2.3 however, in the version 3.3.3, it doesn't work and gives an error message saying ImportError: No module named my_relax.tensor_mc. I was wondering if the module has been renamed/replaced to something else or is this something entirely different
Re: diffusion tensor
Hi Angelo, I'm not sure if you have seen this as you may not be subscribed to the relax-announce mailing list (https://mail.gna.org/listinfo/relax-announce), but a new version of relax has been released fixing the bugs you have encountered. The following link describes the different ways in which you can find out about new relax releases: http://article.gmane.org/gmane.science.nmr.relax.user/1413 Regards, Edward On 13 March 2013 18:15, Edward d'Auvergne edw...@nmr-relax.com wrote: Hi, Have you tried Sebastien Morin's consistency testing analysis which is in relax (http://www.nmr-relax.com/manual/Consistency_testing.html)? This might tell you if there are problems with your relaxation data. I would assume that you have used proper per-experiment temperature calibration using MeOH/ethylene glycol and single-scan interleaving for temperature control: http://www.nmr-relax.com/manual/Temperature_control_calibration.html And that you have used the appropriate spectral processing and peak height extraction: http://www.nmr-relax.com/manual/From_spectra_peak_intensities_relaxation_rates.html These links are from the HTML version of the relax manual (http://www.nmr-relax.com/manual/index.html). Note that the error analysis is incredibly important - I always say that accuracy in the errors is just as important, or maybe even more important, than the data itself. If the errors are wrong, then the results from any type of modelling analysis will be meaningless (there are shelves in maths libraries dedicated to this large field of mathematics: http://en.wikipedia.org/wiki/Mathematical_model) . Assuming you have done all of this, then there could be other issues affecting the analysis. Did you collect all data on a single sample and, if not, did you make sure the protein concentration was identical in each sample? Partial dimerisation, even non-specific and at very low percentages, could significantly affect the analysis. Even more so if slightly different sample concentrations are used. Did you use all of the global diffusion models in the model-free analysis? Are the AIC values significantly different between the models? Also, did you use relax to calculate the R1 and R2 relaxation rates and the NOE? Note that almost no protein will tumble as a perfect sphere. You can see this with the inertia tensor, and almost no model-free analysis using today's methodology will select the spherical tensor. One part that you don't see, which is a very significant part of the diffusion tensor, is the water shell. This can have different thicknesses around your system depending upon surface hydrophobicity/hydrophilicity, the presence of charges, bound metals (even a loose attraction), and loop and other internal motions. So even a perfect mathematical sphere with different localised surface properties will not diffuse as a sphere. Anyway, I hope some of this information helps. Regards, Edward On 13 March 2013 17:31, Angelo Miguel Figueiredo am.figueir...@fct.unl.pt wrote: Sorry once again. In fact relax has chosen the 'local_tm however I don't get any diffusion tensor even selecting on the user function menu the diffusion_tensor.display says: RelaxError: No diffusion tensor data exists I think this might be normal for the local_tm model once it assumes the molecule doesn't diffuse as a globular protein and somehow none of the models fits the data?! However, this result is quite strange since my protein is quite spherical and the inertia tensors are 1: 0.8: 0.7 Any ideas? many thanks, Angelo On 13 Mar 2013, at 13:07, Edward d'Auvergne wrote: Hi Angelo, Welcome to the relax mailing lists! The problem you are seeing is a clear bug. Would you be able to submit a bug report using the link https://gna.org/bugs/?func=additemgroup=relax ? Thanks. Although bug #12408 (https://gna.org/bugs/?12408) appears to be similar, this is only because both cases use the special RelaxNoTensorError error object. For the bug report, would you be able to include the output of: $ relax --info Also if you could look at the logs and say which global diffusion model was selected, that would be useful. And have you used a 3D structure file for the analysis? Note that this failure has occurred at the very end of the analysis. The call to the structure.create_diff_tensor_pdb user function is the very last thing that this model-free auto-analysis does (you can see that here if you are interested, http://www.nmr-relax.com/api/auto_analyses.dauvergne_protocol-pysrc.html#dAuvergne_protocol.execute). Therefore this error is not too important for your analysis. It would be good to have the bug report though so that I can come up with a solution. Cheers, Edward On 13 March 2013 13:43, Angelo Miguel Figueiredo am.figueir...@fct.unl.pt wrote: Dear relax community, I am a new user that recently installed relax 2.2.2. After been playing
diffusion tensor
Dear relax community,
I am a new user that recently installed relax 2.2.2. After been playing around
with it I spot in the late stage of my final calculation the following message
in attach.
Does anybody has a clue or advice what could be wrong with it. I spot a similar
error in earlier relax versions (bug #12408) but I am not sure if it is the
same issue, apparently relax can't read/load my diffusion tensor.
Any help will be appreciated.
Many thanks,
Angelo
relax structure.create_diff_tensor_pdb(scale=1.8e-06, file='tensor.pdb',
dir='/home/final', force=True)
Exception raised in thread.
Traceback (most recent call last):
File /home/angelo/Software/relax-2.2.2/gui/analyses/execute.py, line 87, in
run
self.run_analysis()
File /home/angelo/Software/relax-2.2.2/gui/analyses/auto_model_free.py, line
808, in run_analysis
dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name,
pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir,
diff_model=self.data.global_models, mf_models=self.data.mf_models,
local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc,
diff_tensor_grid_inc=self.data.diff_tensor_grid_inc,
mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter,
conv_loop=self.data.conv_loop)
File /home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py,
line 234, in __init__
self.execute()
File /home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py,
line 745, in execute
self.write_results()
File /home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py,
line 937, in write_results
self.interpreter.structure.create_diff_tensor_pdb(file=tensor.pdb, dir=dir,
force=True)
File /home/angelo/Software/relax-2.2.2/prompt/uf_objects.py, line 219, in
__call__
self._backend(*new_args, **uf_kargs)
File /home/angelo/Software/relax-2.2.2/generic_fns/structure/geometric.py,
line 449, in create_diff_tensor_pdb
raise RelaxNoTensorError('diffusion')
RelaxNoTensorError: RelaxError: No diffusion tensor data exists.___
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relax-users@gna.org
To unsubscribe from this list, get a password
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visit the list information page at
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Re: diffusion tensor
Hi Angelo,
Welcome to the relax mailing lists! The problem you are seeing is a
clear bug. Would you be able to submit a bug report using the link
https://gna.org/bugs/?func=additemgroup=relax ? Thanks. Although
bug #12408 (https://gna.org/bugs/?12408) appears to be similar, this
is only because both cases use the special RelaxNoTensorError error
object. For the bug report, would you be able to include the output
of:
$ relax --info
Also if you could look at the logs and say which global diffusion
model was selected, that would be useful. And have you used a 3D
structure file for the analysis?
Note that this failure has occurred at the very end of the analysis.
The call to the structure.create_diff_tensor_pdb user function is the
very last thing that this model-free auto-analysis does (you can see
that here if you are interested,
http://www.nmr-relax.com/api/auto_analyses.dauvergne_protocol-pysrc.html#dAuvergne_protocol.execute).
Therefore this error is not too important for your analysis. It
would be good to have the bug report though so that I can come up with
a solution.
Cheers,
Edward
On 13 March 2013 13:43, Angelo Miguel Figueiredo
am.figueir...@fct.unl.pt wrote:
Dear relax community,
I am a new user that recently installed relax 2.2.2. After been playing
around with it I spot in the late stage of my final calculation the
following message in attach.
Does anybody has a clue or advice what could be wrong with it. I spot a
similar error in earlier relax versions (bug #12408) but I am not sure if it
is the same issue, apparently relax can't read/load my diffusion tensor.
Any help will be appreciated.
Many thanks,
Angelo
relax structure.create_diff_tensor_pdb(scale=1.8e-06, file='tensor.pdb',
dir='/home/final', force=True)
Exception raised in thread.
Traceback (most recent call last):
File /home/angelo/Software/relax-2.2.2/gui/analyses/execute.py, line 87,
in run
self.run_analysis()
File /home/angelo/Software/relax-2.2.2/gui/analyses/auto_model_free.py,
line 808, in run_analysis
dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name,
pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir,
diff_model=self.data.global_models, mf_models=self.data.mf_models,
local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc,
diff_tensor_grid_inc=self.data.diff_tensor_grid_inc,
mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter,
conv_loop=self.data.conv_loop)
File
/home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py,
line 234, in __init__
self.execute()
File
/home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py,
line 745, in execute
self.write_results()
File
/home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py,
line 937, in write_results
self.interpreter.structure.create_diff_tensor_pdb(file=tensor.pdb,
dir=dir, force=True)
File /home/angelo/Software/relax-2.2.2/prompt/uf_objects.py, line 219, in
__call__
self._backend(*new_args, **uf_kargs)
File /home/angelo/Software/relax-2.2.2/generic_fns/structure/geometric.py,
line 449, in create_diff_tensor_pdb
raise RelaxNoTensorError('diffusion')
RelaxNoTensorError: RelaxError: No diffusion tensor data exists.
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Re: diffusion tensor
Sorry once again. In fact relax has chosen the 'local_tm however I don't get
any diffusion tensor even selecting on the user function menu the
diffusion_tensor.display says:
RelaxError: No diffusion tensor data exists
I think this might be normal for the local_tm model once it assumes the
molecule doesn't diffuse as a globular protein and somehow none of the models
fits the data?!
However, this result is quite strange since my protein is quite spherical and
the inertia tensors are 1: 0.8: 0.7
Any ideas?
many thanks,
Angelo
On 13 Mar 2013, at 13:07, Edward d'Auvergne wrote:
Hi Angelo,
Welcome to the relax mailing lists! The problem you are seeing is a
clear bug. Would you be able to submit a bug report using the link
https://gna.org/bugs/?func=additemgroup=relax ? Thanks. Although
bug #12408 (https://gna.org/bugs/?12408) appears to be similar, this
is only because both cases use the special RelaxNoTensorError error
object. For the bug report, would you be able to include the output
of:
$ relax --info
Also if you could look at the logs and say which global diffusion
model was selected, that would be useful. And have you used a 3D
structure file for the analysis?
Note that this failure has occurred at the very end of the analysis.
The call to the structure.create_diff_tensor_pdb user function is the
very last thing that this model-free auto-analysis does (you can see
that here if you are interested,
http://www.nmr-relax.com/api/auto_analyses.dauvergne_protocol-pysrc.html#dAuvergne_protocol.execute).
Therefore this error is not too important for your analysis. It
would be good to have the bug report though so that I can come up with
a solution.
Cheers,
Edward
On 13 March 2013 13:43, Angelo Miguel Figueiredo
am.figueir...@fct.unl.pt wrote:
Dear relax community,
I am a new user that recently installed relax 2.2.2. After been playing
around with it I spot in the late stage of my final calculation the
following message in attach.
Does anybody has a clue or advice what could be wrong with it. I spot a
similar error in earlier relax versions (bug #12408) but I am not sure if it
is the same issue, apparently relax can't read/load my diffusion tensor.
Any help will be appreciated.
Many thanks,
Angelo
relax structure.create_diff_tensor_pdb(scale=1.8e-06, file='tensor.pdb',
dir='/home/final', force=True)
Exception raised in thread.
Traceback (most recent call last):
File /home/angelo/Software/relax-2.2.2/gui/analyses/execute.py, line 87,
in run
self.run_analysis()
File /home/angelo/Software/relax-2.2.2/gui/analyses/auto_model_free.py,
line 808, in run_analysis
dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name,
pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir,
diff_model=self.data.global_models, mf_models=self.data.mf_models,
local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc,
diff_tensor_grid_inc=self.data.diff_tensor_grid_inc,
mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter,
conv_loop=self.data.conv_loop)
File
/home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py,
line 234, in __init__
self.execute()
File
/home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py,
line 745, in execute
self.write_results()
File
/home/angelo/Software/relax-2.2.2/auto_analyses/dauvergne_protocol.py,
line 937, in write_results
self.interpreter.structure.create_diff_tensor_pdb(file=tensor.pdb,
dir=dir, force=True)
File /home/angelo/Software/relax-2.2.2/prompt/uf_objects.py, line 219, in
__call__
self._backend(*new_args, **uf_kargs)
File /home/angelo/Software/relax-2.2.2/generic_fns/structure/geometric.py,
line 449, in create_diff_tensor_pdb
raise RelaxNoTensorError('diffusion')
RelaxNoTensorError: RelaxError: No diffusion tensor data exists.
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Re: diffusion tensor
Hi, Have you tried Sebastien Morin's consistency testing analysis which is in relax (http://www.nmr-relax.com/manual/Consistency_testing.html)? This might tell you if there are problems with your relaxation data. I would assume that you have used proper per-experiment temperature calibration using MeOH/ethylene glycol and single-scan interleaving for temperature control: http://www.nmr-relax.com/manual/Temperature_control_calibration.html And that you have used the appropriate spectral processing and peak height extraction: http://www.nmr-relax.com/manual/From_spectra_peak_intensities_relaxation_rates.html These links are from the HTML version of the relax manual (http://www.nmr-relax.com/manual/index.html). Note that the error analysis is incredibly important - I always say that accuracy in the errors is just as important, or maybe even more important, than the data itself. If the errors are wrong, then the results from any type of modelling analysis will be meaningless (there are shelves in maths libraries dedicated to this large field of mathematics: http://en.wikipedia.org/wiki/Mathematical_model) . Assuming you have done all of this, then there could be other issues affecting the analysis. Did you collect all data on a single sample and, if not, did you make sure the protein concentration was identical in each sample? Partial dimerisation, even non-specific and at very low percentages, could significantly affect the analysis. Even more so if slightly different sample concentrations are used. Did you use all of the global diffusion models in the model-free analysis? Are the AIC values significantly different between the models? Also, did you use relax to calculate the R1 and R2 relaxation rates and the NOE? Note that almost no protein will tumble as a perfect sphere. You can see this with the inertia tensor, and almost no model-free analysis using today's methodology will select the spherical tensor. One part that you don't see, which is a very significant part of the diffusion tensor, is the water shell. This can have different thicknesses around your system depending upon surface hydrophobicity/hydrophilicity, the presence of charges, bound metals (even a loose attraction), and loop and other internal motions. So even a perfect mathematical sphere with different localised surface properties will not diffuse as a sphere. Anyway, I hope some of this information helps. Regards, Edward On 13 March 2013 17:31, Angelo Miguel Figueiredo am.figueir...@fct.unl.pt wrote: Sorry once again. In fact relax has chosen the 'local_tm however I don't get any diffusion tensor even selecting on the user function menu the diffusion_tensor.display says: RelaxError: No diffusion tensor data exists I think this might be normal for the local_tm model once it assumes the molecule doesn't diffuse as a globular protein and somehow none of the models fits the data?! However, this result is quite strange since my protein is quite spherical and the inertia tensors are 1: 0.8: 0.7 Any ideas? many thanks, Angelo On 13 Mar 2013, at 13:07, Edward d'Auvergne wrote: Hi Angelo, Welcome to the relax mailing lists! The problem you are seeing is a clear bug. Would you be able to submit a bug report using the link https://gna.org/bugs/?func=additemgroup=relax ? Thanks. Although bug #12408 (https://gna.org/bugs/?12408) appears to be similar, this is only because both cases use the special RelaxNoTensorError error object. For the bug report, would you be able to include the output of: $ relax --info Also if you could look at the logs and say which global diffusion model was selected, that would be useful. And have you used a 3D structure file for the analysis? Note that this failure has occurred at the very end of the analysis. The call to the structure.create_diff_tensor_pdb user function is the very last thing that this model-free auto-analysis does (you can see that here if you are interested, http://www.nmr-relax.com/api/auto_analyses.dauvergne_protocol-pysrc.html#dAuvergne_protocol.execute). Therefore this error is not too important for your analysis. It would be good to have the bug report though so that I can come up with a solution. Cheers, Edward On 13 March 2013 13:43, Angelo Miguel Figueiredo am.figueir...@fct.unl.pt wrote: Dear relax community, I am a new user that recently installed relax 2.2.2. After been playing around with it I spot in the late stage of my final calculation the following message in attach. Does anybody has a clue or advice what could be wrong with it. I spot a similar error in earlier relax versions (bug #12408) but I am not sure if it is the same issue, apparently relax can't read/load my diffusion tensor. Any help will be appreciated. Many thanks, Angelo relax structure.create_diff_tensor_pdb(scale=1.8e-06, file='tensor.pdb', dir='/home/final', force=True) Exception raised in thread. Traceback (most
Re: Spheroid diffusion tensor
Hi Ed,
Thanks for this info !
Cheers,
Séb
Edward d'Auvergne wrote:
Hi,
The internal representation in relax is {tm, Da, theta, phi}, so this
is how it is output in the results file. All the different types of
parameter which are input are converted to this internal
representations. If you need, there are user functions which will
convert between the formats, printing out the different parameters.
Regards,
Edward
On Feb 8, 2008 5:39 PM, Sebastien Morin [EMAIL PROTECTED] wrote:
Hi,
I am trying to select a prolate spheroid diffusion tensor.
I want to specify the Dratio, so I chose 'param_types=2' ('tm',
'Dratio', 'Theta', 'Phi') :
===
diffusion_tensor.init(name, (12.41e-9, 1.23, 0, 0i), param_types=2,
spheroid_type='prolate', fixed=1)
===
It seems to work without erros. However, when I look in the results
file, I can only see 'tm', 'Da', 'Theta' and 'Phi' (in the header).
Is it normal or should 'Dratio' show up (since I specified I wanted to
work with this parameter instead) ?
Thanks !
Séb
--
Sebastien Morin
Etudiant au PhD en biochimie
Laboratoire de resonance magnetique nucleaire
Dr Stephane Gagne
CREFSIP (Universite Laval, Quebec, CANADA)
1-418-656-2131 #4530
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--
Sebastien Morin
Etudiant au PhD en biochimie
Laboratoire de resonance magnetique nucleaire
Dr Stephane Gagne
CREFSIP (Universite Laval, Quebec, CANADA)
1-418-656-2131 #4530
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The use of a pdb with the sphere diffusion tensor
Hi, I am now helping someone to start with relax and got into a question about the full_analysis.py script. In the full_analysis.py script, the following code appears at line 550 : # Load the PDB file. if not local_tm: pdb(name, PDB_FILE) For a local tm, no PDB file is needed. That's logic. However, I would have thought that no pdb file would also be needed for an isotropic diffusion tensor (sphere). Am I right ? Can someone with no 3D structure use the full_analysis.py script to optimize an isotropic diffusion tensor ? Thanks ! Sébastien :) ___ relax (http://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/listinfo/relax-users
Re: The use of a pdb with the sphere diffusion tensor
Done! See https://mail.gna.org/public/relax-commits/2008-01/msg00376.html. The current version of the script in the 1.2 line will now properly handle not having a PDB file if you set the value of PDB_FILE to None. Nevertheless, I would be very careful with the conclusions. If there are regions appearing to exhibit chemical exchange or slow nanosecond motions - check very carefully that these motions are also present in the local tm model MI results. If not, there is a good chance that you have artificial motions! Regards, Edward On Jan 10, 2008 8:20 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Hi, I am now helping someone to start with relax and got into a question about the full_analysis.py script. In the full_analysis.py script, the following code appears at line 550 : # Load the PDB file. if not local_tm: pdb(name, PDB_FILE) For a local tm, no PDB file is needed. That's logic. However, I would have thought that no pdb file would also be needed for an isotropic diffusion tensor (sphere). Am I right ? Can someone with no 3D structure use the full_analysis.py script to optimize an isotropic diffusion tensor ? Thanks ! Sébastien :) ___ relax (http://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/listinfo/relax-users ___ relax (http://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/listinfo/relax-users
Re: The use of a pdb with the sphere diffusion tensor
A question re: unresolved residues. Is it necessary to list unresolved residues in this file if no data was supplied for these residues? Example r1 file (made up): 1 2 3 2.7114 0.05 4. 2.6151 0.04 Do residues 1 and 2 need to be listed in the unresolved file? Thanks, Doug On Jan 10, 2008, at 3:59 PM, Sebastien Morin wrote: Thanks Ed ! Another similar would maybe ease life of users without PDB or with small proteins... We could add the possibility of not having any file for unresolved residues... The lines : = # The file containing the list of unresolved residues to exclude from the analysis. UNRES = 'unresolved' = could become : = # The file containing the list of unresolved residues to exclude from the analysis (set this to None if no residue is to be excluded). UNRES = 'None' = and the lines : = # Unselect unresolved residues. unselect.read(name, file=UNRES) = could become : = # Unselect unresolved residues. if not UNRES: unselect.read(name, file=UNRES) = This would avoid using an empty file for (non existant) unresolved residues or commenting 2 different lines in the code... If you agree, I could make the change right away... Ciao ! Sébastien Edward d'Auvergne wrote: Done! See https://mail.gna.org/public/relax-commits/2008-01/ msg00376.html. The current version of the script in the 1.2 line will now properly handle not having a PDB file if you set the value of PDB_FILE to None. Nevertheless, I would be very careful with the conclusions. If there are regions appearing to exhibit chemical exchange or slow nanosecond motions - check very carefully that these motions are also present in the local tm model MI results. If not, there is a good chance that you have artificial motions! Regards, Edward On Jan 10, 2008 8:20 PM, Sebastien Morin sebastien.morin. [EMAIL PROTECTED] wrote: Hi, I am now helping someone to start with relax and got into a question about the full_analysis.py script. In the full_analysis.py script, the following code appears at line 550 : # Load the PDB file. if not local_tm: pdb(name, PDB_FILE) For a local tm, no PDB file is needed. That's logic. However, I would have thought that no pdb file would also be needed for an isotropic diffusion tensor (sphere). Am I right ? Can someone with no 3D structure use the full_analysis.py script to optimize an isotropic diffusion tensor ? Thanks ! Sébastien :) ___ relax (http://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/listinfo/relax-users -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP (Universite Laval, Quebec, CANADA) 1-418-656-2131 #4530 ___ relax (http://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/listinfo/relax-users ___ relax (http://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/listinfo/relax-users
Re: The use of a pdb with the sphere diffusion tensor
On Jan 10, 2008 10:06 PM, Douglas Kojetin [EMAIL PROTECTED] wrote: A question re: unresolved residues. Is it necessary to list unresolved residues in this file if no data was supplied for these residues? Example r1 file (made up): 1 2 3 2.7114 0.05 4. 2.6151 0.04 Do residues 1 and 2 need to be listed in the unresolved file? No, these will not be used by relax as they will have no data. Regards, Edward ___ relax (http://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/listinfo/relax-users
Re: The use of a pdb with the sphere diffusion tensor
I tried the line a you proposed : UNRES = None and it yields an error. relax unselect.read(run='tm0', file=None, dir=None, change_all=0, column=0) RelaxError: The file name argument None must be a string. However, UNRES = 'None' does not yield this error and the script proceeds... Am I right ? Séb :) Edward d'Auvergne wrote: On Jan 10, 2008 9:59 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Thanks Ed ! Another similar would maybe ease life of users without PDB or with small proteins... We could add the possibility of not having any file for unresolved residues... The lines : = # The file containing the list of unresolved residues to exclude from the analysis. UNRES = 'unresolved' = could become : = # The file containing the list of unresolved residues to exclude from the analysis (set this to None if no residue is to be excluded). UNRES = 'None' = This should be: UNRES = None rather than a string. The user will instantly see the problem if 'None' is supplied as a string. But this is a good idea, so feel free to make the changes. Don't forget to port the changes to the 1.3 line using 'svn merge'. Regards, Edward -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP (Universite Laval, Quebec, CANADA) 1-418-656-2131 #4530 ___ relax (http://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/listinfo/relax-users
Re: The use of a pdb with the sphere diffusion tensor
Actually, the test you proposed: = # Unselect unresolved residues. if not UNRES: unselect.read(name, file=UNRES) = should not include not. The statement needed is that if the UNRES file exists, use it to deselect the residues. It currently say that if the UNRES file does not exist, use it to deselect the residues. Sorry, I should have seen that one. Regards, Edward On Jan 10, 2008 10:17 PM, Sebastien Morin [EMAIL PROTECTED] wrote: I tried the line a you proposed : UNRES = None and it yields an error. relax unselect.read(run='tm0', file=None, dir=None, change_all=0, column=0) RelaxError: The file name argument None must be a string. However, UNRES = 'None' does not yield this error and the script proceeds... Am I right ? Séb :) Edward d'Auvergne wrote: On Jan 10, 2008 9:59 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Thanks Ed ! Another similar would maybe ease life of users without PDB or with small proteins... We could add the possibility of not having any file for unresolved residues... The lines : = # The file containing the list of unresolved residues to exclude from the analysis. UNRES = 'unresolved' = could become : = # The file containing the list of unresolved residues to exclude from the analysis (set this to None if no residue is to be excluded). UNRES = 'None' = This should be: UNRES = None rather than a string. The user will instantly see the problem if 'None' is supplied as a string. But this is a good idea, so feel free to make the changes. Don't forget to port the changes to the 1.3 line using 'svn merge'. Regards, Edward -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP (Universite Laval, Quebec, CANADA) 1-418-656-2131 #4530 ___ relax (http://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/listinfo/relax-users
Re: The use of a pdb with the sphere diffusion tensor
Hi, You're right. Sorry for that... It is corrected in r4620. Séb Edward d'Auvergne wrote: Actually, the test you proposed: = # Unselect unresolved residues. if not UNRES: unselect.read(name, file=UNRES) = should not include not. The statement needed is that if the UNRES file exists, use it to deselect the residues. It currently say that if the UNRES file does not exist, use it to deselect the residues. Sorry, I should have seen that one. Regards, Edward On Jan 10, 2008 10:17 PM, Sebastien Morin [EMAIL PROTECTED] wrote: I tried the line a you proposed : UNRES = None and it yields an error. relax unselect.read(run='tm0', file=None, dir=None, change_all=0, column=0) RelaxError: The file name argument None must be a string. However, UNRES = 'None' does not yield this error and the script proceeds... Am I right ? Séb :) Edward d'Auvergne wrote: On Jan 10, 2008 9:59 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Thanks Ed ! Another similar would maybe ease life of users without PDB or with small proteins... We could add the possibility of not having any file for unresolved residues... The lines : = # The file containing the list of unresolved residues to exclude from the analysis. UNRES = 'unresolved' = could become : = # The file containing the list of unresolved residues to exclude from the analysis (set this to None if no residue is to be excluded). UNRES = 'None' = This should be: UNRES = None rather than a string. The user will instantly see the problem if 'None' is supplied as a string. But this is a good idea, so feel free to make the changes. Don't forget to port the changes to the 1.3 line using 'svn merge'. Regards, Edward -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP (Universite Laval, Quebec, CANADA) 1-418-656-2131 #4530 -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP (Universite Laval, Quebec, CANADA) 1-418-656-2131 #4530 ___ relax (http://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/listinfo/relax-users
initial estimate of the diffusion tensor
Hi, In the following post [https://mail.gna.org/public/relax-users/ 2007-05/msg9.html], Edward said that relax could be used to estimate the diffusion tensor parameters (instead of using the program Tensor). Does this protocol already exist in the form of a python script? If not, could someone briefly outline the protocol in an email so I can write it myself? Thanks, Doug ___ relax (http://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/listinfo/relax-users
Diffusion tensor figure.
Hi, That's no problem. The script for this diffusion tensor image is called diff_tensor_pdb.py. It can be found in the 1.3 line. The only currently functional version of relax capable of making this figure is relax-1.3.0, so I would recommend installing that version as well and looking in the 'sample_scripts/' directory. This script handles spherical, spheroidal, and ellipsoidal diffusion tensors. Regards, Edward On Sun, 2007-12-09 at 11:04 -0500, Douglas Kojetin wrote: Hi Edward, Thanks for this. Would you also be willing to share the script used to create Figure 7.5: The Brownian rotational diffusion tensor of OMP as determined by the new model-free optimisation protocol ? Thanks, Doug On Dec 9, 2007, at 9:49 AM, Edward d'Auvergne wrote: Hi, I didn't include the XH bond distribution scripts with relax. There were a couple of these to generate the figure. These 2 file have been attached to this message. 'dist.py' generates parts c and d whereas 'dist_core.py' generates parts a and b. For those who are interested, this figure is from my PhD thesis located at http://eprints.infodiv.unimelb.edu.au/archive/2799/. Note that the file 'core' referred to in 'dist_core.py' is just a text file with one residue number per line. Also, depending on how you look at these scripts, be careful and maybe remove any line wrapping. I hope you find this useful. Regards, Edward On Mon, 2007-12-03 at 12:26 -0500, Douglas Kojetin wrote: Hi Edward, Is a relax script available that creates a PyMOL (or MOLMOL) structure figure of the NH bond vector orientations, as shown in your dissertation (Figure 7.8; page 252)? Thanks, Dougdist_core.pydist.py ___ relax (http://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/listinfo/relax-users
diffusion tensor related
Dear relax users, I am trying to run relax using spheroid model. I am a bit confused how to set diffusion tensor. I tried r2r1_diffusion to get Diso and Dper and Dpar, Theta and Phi, then input these values into the script (sample_script/model-free.py) and in this script diffusion_tensor.init(name, (2e-8, 1.3, 60, 290), param_types=0, spheroid_type='prolate', fixed=1) I guess the values should be tm and Da, theta and Phi (is the second value 1.3 Da? seems not right cause I got 5e7 for this) what do the flages mean? I tried to change param_types=0 to 1, relax will require me to change tm to Diso. Again if I change fixed from 1 to 0, relax will encounte problems with GridsearchSize too big error and stop. How should I set the diffusion tensor?Does it means if fixed=1, the diffusion tensor I input should be fixed? But I checked results that the Theta and Phi still varied. I would be very much appreciate any suggestions! Hongyan Dr. Hongyan Li Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong ___ relax (http://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/listinfo/relax-users
Diffusion Tensor - Global correlation time
Hi ! I have a question about the diffusion tensor and the global correlation time. Palmer proposes to estimate the diffusion tensor and global correlation tensor as what follows : 1. Use pdbinertia with the 3D structure to get the moments of inertia. 2. Use r2r1_diffusion with the R2/R1 values and 3D structure to estimate the diffusion tensor type and values (isotropic, axial, anisotropic, Diso, Dpar, Dper, etc) and associated global correlation time (tm). 3. Confirm these values obtained by r2r1_diffusion with quadric using local correlation times obtained with r2r1_tm. When one possesses estimated values for his molecule, the next step is to use Model-Free with those values and select the models. At the end, a global optimization is performed (the diffusion tensor and the global correlation time are then optimized)... === What is the best way to estimate (and optimize) the diffusion tensor and global correlation time using the relax approach ? Thanks for helping me getting started with this promising program ! Séb -- __ ___ | | || Sebastien Morin || ||| Etudiant au doctorat en biochimie ||| Laboratoire de resonance magnetique nucleaire | Dr Stephane Gagne | CREFSIP (Universite Laval) ||| 1-418-656-2131 poste 4530 ||| || [EMAIL PROTECTED] || |___| __ ___ relax (http://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/listinfo/relax-users
