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Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval
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From: Kanika K. <kha...@gm...> - 2016-02-23 21:11:53
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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 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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--
Best
Kanika Khanna
Graduate Student, Biological Sciences Department
University of California, San Diego
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