Dear Edward
Thanks a lot for the reply.. The hard disk on my desktop is fine and there is plenty of storage space on it. I have attached the results.bz2 file with this email as I couldn't login to my account which further didn't allow me to generate a bug report. Thanks Ashish ________________________________ From: relax-users <relax-users-boun...@gna.org> on behalf of relax-users-requ...@gna.org <relax-users-requ...@gna.org> Sent: Tuesday, February 21, 2017 7:00:51 PM To: relax-users@gna.org Subject: relax-users Digest, Vol 120, Issue 3 Send relax-users mailing list submissions to relax-users@gna.org To subscribe or unsubscribe via the World Wide Web, visit https://mail.gna.org/listinfo/relax-users or, via email, send a message with subject or body 'help' to relax-users-requ...@gna.org You can reach the person managing the list at relax-users-ow...@gna.org When replying, please edit your Subject line so it is more specific than "Re: Contents of relax-users digest..." Today's Topics: 1. Error in setting up model free analysis (Ashish Sethi) 2. Error in setting up model free analysis (Ashish Sethi) 3. Re: Error in setting up model free analysis (Ashish Sethi) 4. Re: Error in setting up model free analysis (Edward d'Auvergne) 5. Re: Error in setting up model free analysis (Edward d'Auvergne) ---------------------------------------------------------------------- Message: 1 Date: Tue, 21 Feb 2017 15:37:28 +1100 From: Ashish Sethi <set...@student.unimelb.edu.au> To: relax-users@gna.org Subject: Error in setting up model free analysis Message-ID: <CAB-9y=q8N8hSR==2FhOTC5KDjFF=jujvomm8y2g7ysckdfg...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Dear Edward, Hope this email finds you well !!! I am a beginner in the field of protein dynamics and I wish to do a model free analysis for my protein which is about 72 residues (8.5 kDa). I have calculated the standard R1, R2 and NOE (steady state) parameters and also did the reduced spectral density mapping. My question is related to dipolar relaxation settings while setting up the model free analysis, so all my files (R1, R2 and NOE) only have 15N spin information and if I follow the instructions given in the manual and select "@N" and "@H" i get an error saying no information available for H spin which is obvious. In this case what am I supposed to select ? Apologies for my naivety. Thanks Ashish -- *Ashish Sethi* PhD Candidate Biochemistry and Molecular Biology Bio21 Molecular Science and Biotechnology Institute University of Melbourne (Parkville Campus) 30, Flemington Road, Parkville Victoria 3010, Australia Tel: +61 3 8344 2504 Mob: 0451211055 Email: set...@student.unimelb.edu.au ------------------------------ Message: 2 Date: Tue, 21 Feb 2017 04:40:24 +0000 From: Ashish Sethi <ashish.se...@unimelb.edu.au> To: "relax-users@gna.org" <relax-users@gna.org> Subject: Error in setting up model free analysis Message-ID: <me1pr01mb1427613c85f418f9b0702d61ab...@me1pr01mb1427.ausprd01.prod.outlook.com> Content-Type: text/plain; charset=WINDOWS-1252 Dear Edward, Hope this email finds you well !!! I am a beginner in the field of protein dynamics and I wish to do a model free analysis for my protein which is about 72 residues (8.5 kDa). I have calculated the standard R1, R2 and NOE (steady state) parameters and also did the reduced spectral density mapping. My question is related to dipolar relaxation settings while setting up the model free analysis, so all my files (R1, R2 and NOE) only have 15N spin information and if I follow the instructions given in the manual and select "@N" and "@H"-- i get an error saying no information available for H spin which is obvious. In this case what am I supposed to select ? Apologies for my naivety. Thanks Ashish ------------------------------ Message: 3 Date: Tue, 21 Feb 2017 06:29:47 +0000 From: Ashish Sethi <ashish.se...@unimelb.edu.au> To: "Mahdi, Sam" <sam.mahdi....@my.csun.edu>, "relax-users@gna.org" <relax-users@gna.org> Subject: Re: Error in setting up model free analysis Message-ID: <me1pr01mb1427ffd9e2becc8e9a46571cab...@me1pr01mb1427.ausprd01.prod.outlook.com> Content-Type: text/plain; charset=WINDOWS-1252 Thanks Sam. I did ignore the error message and run the model free analysis and I got the following errors: Traceback (most recent call last): File "/usr/local/relax/gui/analyses/execute.py", line 87, in run self.run_analysis() File "/usr/local/relax/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 "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 241, in __init__ self.execute() File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 604, in execute self.interpreter.results.read(file='results', dir=self.results_dir+'local_tm'+sep+'aic') File "/usr/local/relax/prompt/uf_objects.py", line 221, in __call__ self._backend(*new_args, **uf_kargs) File "/usr/local/relax/generic_fns/results.py", line 96, in read ds.from_xml(file, dir=dirname(file_path), pipe_to=pipes.cdp_name()) File "/usr/local/relax/data/__init__.py", line 452, in from_xml self[pipe_to].from_xml(pipe_nodes[0], dir=dir, file_version=file_version) File "/usr/local/relax/data/pipe_container.py", line 255, in from_xml self.structure.from_xml(str_nodes[0], dir=dir, id=parser, file_version=file_version) File "/usr/local/relax/generic_fns/structure/api_base.py", line 296, in from_xml self.structural_data.from_xml(model_nodes, id=id, file_version=file_version) File "/usr/local/relax/generic_fns/structure/api_base.py", line 1223, in from_xml self[-1].mol.from_xml(mol_nodes, id=id, file_version=file_version) File "/usr/local/relax/generic_fns/structure/api_base.py", line 1441, in from_xml self[-1].from_xml(mol_node, file_version=file_version) File "/usr/local/relax/generic_fns/structure/internal.py", line 2607, in from_xml xml_to_object(mol_node, self, file_version=file_version) File "/usr/local/relax/data/relax_xml.py", line 277, in xml_to_object value[i] = packBytesAsPyFloat(ieee_value[i]) File "/usr/local/relax/float.py", line 200, in packBytesAsPyFloat doubleString=pack('8B',*bytes) error: pack expected 8 items for packing (got 571) Can anyone suggest what is the problem ? Thanks a lot. Ashish ________________________________ From: Mahdi, Sam <sam.mahdi....@my.csun.edu> Sent: Tuesday, February 21, 2017 4:17:08 PM To: Ashish Sethi Subject: Re: Error in setting up model free analysis Hi Ashish, I am not part of Edwards team, just a normal relax user. The error is simply informing you there is no information for hydrogen spins (which there shouldn't be), so its fine. It will exclude the hydrogen spin dynamics in its computations, so there is nothing to worry about in regards to the error (from my experience). Sincerely, Sam On Mon, Feb 20, 2017 at 8:40 PM, Ashish Sethi <ashish.se...@unimelb.edu.au<mailto:ashish.se...@unimelb.edu.au>> wrote: Dear Edward, Hope this email finds you well !!! I am a beginner in the field of protein dynamics and I wish to do a model free analysis for my protein which is about 72 residues (8.5 kDa). I have calculated the standard R1, R2 and NOE (steady state) parameters and also did the reduced spectral density mapping. My question is related to dipolar relaxation settings while setting up the model free analysis, so all my files (R1, R2 and NOE) only have 15N spin information and if I follow the instructions given in the manual and select "@N" and "@H"-- i get an error saying no information available for H spin which is obvious. In this case what am I supposed to select ? Apologies for my naivety. Thanks Ashish _______________________________________________ relax (http://www.nmr-relax.com<http://www.nmr-relax.com>) This is the relax-users mailing list relax-users@gna.org<mailto: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<https://mail.gna.org/listinfo/relax-users> ------------------------------ Message: 4 Date: Tue, 21 Feb 2017 08:53:28 +0100 From: "Edward d'Auvergne" <edw...@nmr-relax.com> To: Ashish Sethi <ashish.se...@unimelb.edu.au> Cc: "relax-users@gna.org" <relax-users@gna.org> Subject: Re: Error in setting up model free analysis Message-ID: <caed9py8vklw5acyolp4eysktfcbz7m2+cgi8onnmvvmbof3...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 On 21 February 2017 at 05:40, Ashish Sethi <ashish.se...@unimelb.edu.au> wrote: > Dear Edward, > > > Hope this email finds you well !!! > > > > I am a beginner in the field of protein dynamics and I wish to do a model > free analysis for my protein which is about 72 residues (8.5 kDa). I have > calculated the standard R1, R2 and NOE (steady state) parameters and also did > the reduced spectral density mapping. > > > My question is related to dipolar relaxation settings while setting up the > model free analysis, so all my files (R1, R2 and NOE) only have 15N spin > information and if I follow the instructions given in the manual and select > "@N" and "@H"-- i get an error saying no information available for H spin > which is obvious. In this case what am I supposed to select ? Apologies for > my naivety. Hi Ashish, Welcome to the relax mailing lists! Note for a model-free analysis that for over 2 decades now it is expected that you collect data at 2 or more field strengths. I suggest you have a read of the following reference to understand why a model-free analysis fails - i.e. you end up with artificial Rex and nanosecond motions: d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. Mol. Biosyst., 3(7), 483-494. (http://dx.doi.org/10.1039/b702202f). As for the error, this should actually be a RelaxWarning saying that the H spins are deselected as there is no relaxation data. If you have a RelaxError, or any other Python Error, could you copy and paste that error message? Otherwise, the RelaxWarning is what you should expect. Regards, Edward ------------------------------ Message: 5 Date: Tue, 21 Feb 2017 09:00:21 +0100 From: "Edward d'Auvergne" <edw...@nmr-relax.com> To: Ashish Sethi <ashish.se...@unimelb.edu.au> Cc: "relax-users@gna.org" <relax-users@gna.org> Subject: Re: Error in setting up model free analysis Message-ID: <CAED9pY9aXXpgpKfJwYGUWKLbZL8yMhTSSXK+9-YXYw=xgnh...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 On 21 February 2017 at 07:29, Ashish Sethi <ashish.se...@unimelb.edu.au> wrote: > Thanks Sam. > > > > I did ignore the error message and run the model free analysis and I got the > following errors: > > > > Traceback (most recent call last): > File "/usr/local/relax/gui/analyses/execute.py", line 87, in run > self.run_analysis() > File "/usr/local/relax/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 "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 241, in > __init__ > self.execute() > File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 604, in > execute > self.interpreter.results.read(file='results', > dir=self.results_dir+'local_tm'+sep+'aic') > File "/usr/local/relax/prompt/uf_objects.py", line 221, in __call__ > self._backend(*new_args, **uf_kargs) > File "/usr/local/relax/generic_fns/results.py", line 96, in read > ds.from_xml(file, dir=dirname(file_path), pipe_to=pipes.cdp_name()) > File "/usr/local/relax/data/__init__.py", line 452, in from_xml > self[pipe_to].from_xml(pipe_nodes[0], dir=dir, file_version=file_version) > File "/usr/local/relax/data/pipe_container.py", line 255, in from_xml > self.structure.from_xml(str_nodes[0], dir=dir, id=parser, > file_version=file_version) > File "/usr/local/relax/generic_fns/structure/api_base.py", line 296, in > from_xml > self.structural_data.from_xml(model_nodes, id=id, > file_version=file_version) > File "/usr/local/relax/generic_fns/structure/api_base.py", line 1223, in > from_xml > self[-1].mol.from_xml(mol_nodes, id=id, file_version=file_version) > File "/usr/local/relax/generic_fns/structure/api_base.py", line 1441, in > from_xml > self[-1].from_xml(mol_node, file_version=file_version) > File "/usr/local/relax/generic_fns/structure/internal.py", line 2607, in > from_xml > xml_to_object(mol_node, self, file_version=file_version) > File "/usr/local/relax/data/relax_xml.py", line 277, in xml_to_object > value[i] = packBytesAsPyFloat(ieee_value[i]) > File "/usr/local/relax/float.py", line 200, in packBytesAsPyFloat > doubleString=pack('8B',*bytes) > error: pack expected 8 items for packing (got 571) > > > > Can anyone suggest what is the problem ? Hi Ashish, Such an error message means that the relax results file is corrupted somehow. Maybe check that you haven't run out of hard disk space or that there are no bad sectors on the hard disk. You could also open up the results_dir+local_tm/aic/results.bz2 file and see if that file looks ok. If there is nothing wrong with your hard disk, could you open up a bug report at https://gna.org/bugs/?func=additem&group=relax and attach the results.bz2 file causing the problem? If you'd like to keep your data private, try deleting residues from the XML file until you only have 1 or 2 left, and use the state.load user function to make sure that that exact "error: pack expected 8 items for packing (got 571)" message is still present. Regards, Edward ------------------------------ Subject: Digest Footer _______________________________________________ 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 ------------------------------ End of relax-users Digest, Vol 120, Issue 3 ******************************************* _______________________________________________ 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