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Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval
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From: Kanika K. <kk...@uc...> - 2016-02-23 21:15:07
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Thanks you for that. When I run the process with openmpi, i get the
following error message:
Open RTE detected a parse error in the hostfile:
/home/kkhanna/Documents/Pytom/Bacillus_ribosome/job.xml
It occured on line number 37 on token 1.
--------------------------------------------------------------------------
[pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file
base/rmaps_base_support_fns.c at line 176
[pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file rmaps_rr.c at
line 121
[pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file
base/rmaps_base_map_job.c at line 379
[pordoi:25878] 2 more processes have sent help message help-hostfile.txt /
parse_error
[pordoi:25878] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages
On Tue, Feb 23, 2016 at 1:11 PM, Kanika Khanna <kha...@gm...>
wrote:
> Thanks you for that. When I run the process with openmpi, i get the
> following error message:
>
> Open RTE detected a parse error in the hostfile:
> /home/kkhanna/Documents/Pytom/Bacillus_ribosome/job.xml
> It occured on line number 37 on token 1.
> --------------------------------------------------------------------------
> [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file
> base/rmaps_base_support_fns.c at line 176
> [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file rmaps_rr.c at
> line 121
> [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file
> base/rmaps_base_map_job.c at line 379
> [pordoi:25878] 2 more processes have sent help message help-hostfile.txt /
> parse_error
> [pordoi:25878] Set MCA parameter "orte_base_help_aggregate" to 0 to see
> all help / error messages
>
>
> On Tue, Feb 23, 2016 at 9:36 AM, Thomas Hrabe <th...@gm...> wrote:
>
>> Hi Kanika,
>>
>> 1. Thanks Dustin, that’s right. You created a job with localizationJob,
>> now you have to run it with localization.py and parallel with mpirun.
>>
>> 2. I think all files I sent are densities and the -s and -v parameters
>> are numeric values and not a boolean expression? I think I do not
>> understand exactly what you mean.
>>
>> Thomas
>>
>>
>> > On Feb 22, 2016, at 5:38 PM, Dustin Morado <dus...@gm...>
>> wrote:
>> >
>> > Kanika,
>> >
>> > The command you used just produces the localization job file and a
>> script to run it. You should now have two files: job.xml and job.sh.
>> >
>> > You do the actual localization by running the command
>> >
>> > mpirun --hostfile "pathToYourHostfile" -c "numberOfCPUs" pytom
>> localization.py job.xml 2 2 2
>> >
>> > which should be similar to what’s in job.sh.
>> >
>> > HTH
>> >
>> > —
>> > Cheers,
>> > Dustin
>> >
>> >> Date: Mon, 22 Feb 2016 17:19:07 -0800
>> >> From: Kanika Khanna <kk...@uc...>
>> >> Subject: Re: [Pytom-mail] Pytom-mail post from
>> >> kha...@gm... requires approval
>> >> To: Thomas Hrabe <th...@gm...>
>> >> Cc: pyt...@li...
>> >> Message-ID:
>> >> <CAA+6D-4uC_p9WSKePOaaCXvy-vGsU94AAezctQUmQQRb=
>> PP...@ma...>
>> >> Content-Type: text/plain; charset="utf-8"
>> >>
>> >> Hello Thomas
>> >>
>> >> 1. I have submitted the job for localization using command line and
>> haven't
>> >> really gotten any result files (scores.em/angles.em)
>> >>
>> >> This is the command I entered as per the tutorial:
>> >>
>> >> localizationJob.py -v tomogram.mrc -r emdb.mrc -m mask.em --wedge1 30
>> >> --wedge2 30 -a angles_12.85_7112.em -d /home/kkhanna/Documents/Pytom/
>> -b 0
>> >> --splitX 2 --splitY 2 -j job.xml
>> >>
>> >> Do you want me to send the tomogram/reference file etc.?
>> >> When I had run the command, there wasn't any error either.
>> >>
>> >> 2. Also, in the previous mail, you sent the .em files for PDBs. Thanks
>> for
>> >> that. I notice that the files with individual chains 3uzoA.em and
>> 3uzoB.em
>> >> are in cubes and the full file 3uzofull.em is density map. When I try
>> to
>> >> generate the EM files with pdb2em, the option to enter the cube size
>> is a
>> >> strict yes. How is it then possible to generate the files with EM map
>> and
>> >> which files are supposed to be used for localization in that case?
>> >>
>> >> Thanks!
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> On Thu, Feb 18, 2016 at 3:19 PM, Thomas Hrabe <th...@gm...>
>> wrote:
>> >>
>> >>> Hi Kanika,
>> >>>
>> >>> the link to the chimera plugin with installation tutorial is back up:
>> >>>
>> >>> http://www.biochem.mpg.de/309018/PyTom
>> >>>
>> >>> Best,
>> >>> Thomas
>> >>>
>> >>> On Feb 18, 2016, at 1:47 PM, Thomas Hrabe <th...@gm...> wrote:
>> >>>
>> >>> Hi Kanika,
>> >>>
>> >>> Thank you for your interest in pytom.
>> >>>
>> >>> 1. It seems that the atomList is empty -> devision by zero from what
>> I can
>> >>> tell from your error. By the way, are you sure you have old style PDB
>> files
>> >>> or the new mmCIF file format (the new ones are not compatible yet, or
>> at
>> >>> least in development are)
>> >>>
>> >>> 2. the scores and angles should be in the result folder you specify.
>> >>>
>> >>> I just checked the Chimera plugin page on the Foerster group page.
>> >>> We will update the links soon.
>> >>>
>> >>> Thanks,
>> >>> Thomas
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> On Feb 18, 2016, at 1:32 PM, pyt...@li...
>> wrote:
>> >>>
>> >>> As list administrator, your authorization is requested for the
>> >>> following mailing list posting:
>> >>>
>> >>> List: Pyt...@li...
>> >>> From: kha...@gm...
>> >>> Subject: Particle extraction and pdb2em
>> >>> Reason: Post by non-member to a members-only list
>> >>>
>> >>> At your convenience, visit:
>> >>>
>> >>> https://lists.sourceforge.net/lists/admindb/pytom-mail
>> >>>
>> >>> to approve or deny the request.
>> >>>
>> >>> *From: *Kanika Khanna <kha...@gm...>
>> >>> *Subject: **Particle extraction and pdb2em*
>> >>> *Date: *February 18, 2016 at 1:31:48 PM PST
>> >>> *To: *pyt...@li...
>> >>>
>> >>>
>> >>> Hello,
>> >>>
>> >>> I am new to pytom and have the following questions:
>> >>>
>> >>> 1. pdb2em: I type in the following to convert my pdb file to em file:
>> >>>
>> >>> pdb2em.py -p "pathtopdbfile" -s 4 -v 50 -o "pathtoemfile" and get the
>> >>> following error message:
>> >>> Traceback (most recent call last):
>> >>> File "/usr/local/pytom/bin/pdb2em.py", line 41, in <module>
>> >>> volume = pdb2em(pdbFile, float(pixelSize), int(cubeSize), chain =
>> >>> chain,densityNegative = densityNegative)
>> >>> File "/usr/local/pytom/basic/files.py", line 369, in pdb2em
>> >>> return atomList2em(atomList,pixelSize,cubeSize,densityNegative)
>> >>> File "/usr/local/pytom/basic/files.py", line 297, in atomList2em
>> >>> centroidX = centroidX / len(atomList)
>> >>> ZeroDivisionError: integer division or modulo by zero
>> >>>
>> >>>
>> >>> Any ideas as to what might be wrong?
>> >>>
>> >>> 2. Once we have the localization file created as .xml and .sh file,
>> how do
>> >>> we get the scores.em and angles.em file for particle extraction? How
>> to
>> >>> visualize these files in chimera using the plugin mentioned in your
>> website
>> >>> (volumedialog_new.py)?
>> >>>
>> >>> Thanks!
>> >>>
>> >>> --
>> >>> Best
>> >>> Kanika Khanna
>> >>> Graduate Student, Biological Sciences Department
>> >>> University of California, San Diego
>> >>>
>> >>>
>> >>>
>> >>> *From: *pyt...@li...
>> >>> *Subject: **confirm 6616e7ea858ae6f8d6a87e73a557d843a511c7d5*
>> >>>
>> >>>
>> >>> If you reply to this message, keeping the Subject: header intact,
>> >>> Mailman will discard the held message. Do this if the message is
>> >>> spam. If you reply to this message and include an Approved: header
>> >>> with the list password in it, the message will be approved for posting
>> >>> to the list. The Approved: header can also appear in the first line
>> >>> of the body of the reply.
>> >>>
>> >>>
>> >>>
>> >>>
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>> >
>> >
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>
>
> --
> Best
> Kanika Khanna
> Graduate Student, Biological Sciences Department
> University of California, San Diego
>
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