pytom-mail — PyTom mailing list for updates and other issues

Re: [Pytom-mail] Tutorial files

[Thomas H. <th...@gm...>]

Hi Kanika,

can you please send the full terminal command and output you processed?

Thomas

> On Feb 24, 2016, at 10:13 AM, Kanika Khanna <kk...@uc...> wrote:
> 
> Hi,
> 
> I downloaded the tutorial file.
> 
> I have been trying to use it to reconstruct the tutorial data and I get the following error when I run the script reconstructTomo.
> 
> sys.version_info(major=2, minor=7, micro=5, releaselevel='final', serial=0)
> option --tiltSeriesPath not recognized
> 
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
> Pytom-mail mailing list
> Pyt...@li...
> https://lists.sourceforge.net/lists/listinfo/pytom-mail

[Pytom-mail] Tutorial files

[Kanika K. <kk...@uc...>]

Hi,

I downloaded the tutorial file.

I have been trying to use it to reconstruct the tutorial data and I get the
following error when I run the script reconstructTomo.



*sys.version_info(major=2, minor=7, micro=5, releaselevel='final',
serial=0)option --tiltSeriesPath not recognized*

Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

[Dustin M. <dus...@gm...>]

Hi Kanika,

What was the command you ran exactly? It looks like there’s an error with your host file. Are you running this on a cluster, or just a workstation with openmpi?

If it’s the latter you can simply run it like this:
mpirun --hostfile localhost -c 8 pytomlocalization.py job.xml 2 2 2

which will send one of each of the 8 chunks of the tomogram to a processor. 

If you are on a cluster, you might want to ask the cluster admin if there’s a specific submit script you need to run to have access to the correct default hostfile.

—
Cheers,
Dustin


> 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 

Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

[Kanika K. <kk...@uc...>]

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.
>> >>>
>> >>>
>> >>>
>> >>>
>> >> -------------- next part --------------
>> >> An HTML attachment was scrubbed...
>> >>
>> >> ------------------------------
>> >>
>> >>
>> ------------------------------------------------------------------------------
>> >> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> >> Monitor end-to-end web transactions and take corrective actions now
>> >> Troubleshoot faster and improve end-user experience. Signup Now!
>> >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> >>
>> >> ------------------------------
>> >>
>> >> _______________________________________________
>> >> Pytom-mail mailing list
>> >> Pyt...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>> >>
>> >>
>> >> End of Pytom-mail Digest, Vol 97, Issue 1
>> >> *****************************************
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> > Monitor end-to-end web transactions and take corrective actions now
>> > Troubleshoot faster and improve end-user experience. Signup Now!
>> > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> > _______________________________________________
>> > Pytom-mail mailing list
>> > Pyt...@li...
>> > https://lists.sourceforge.net/lists/listinfo/pytom-mail
>>
>>
>
>
> --
> Best
> Kanika Khanna
> Graduate Student, Biological Sciences Department
> University of California, San Diego
>

Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

[Kanika K. <kha...@gm...>]

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.
> >>>
> >>>
> >>>
> >>>
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >>
> >> ------------------------------
> >>
> >>
> ------------------------------------------------------------------------------
> >> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> >> Monitor end-to-end web transactions and take corrective actions now
> >> Troubleshoot faster and improve end-user experience. Signup Now!
> >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> >>
> >> ------------------------------
> >>
> >> _______________________________________________
> >> Pytom-mail mailing list
> >> Pyt...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pytom-mail
> >>
> >>
> >> End of Pytom-mail Digest, Vol 97, Issue 1
> >> *****************************************
> >
> >
> >
> ------------------------------------------------------------------------------
> > Site24x7 APM Insight: Get Deep Visibility into Application Performance
> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> > Monitor end-to-end web transactions and take corrective actions now
> > Troubleshoot faster and improve end-user experience. Signup Now!
> > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> > _______________________________________________
> > Pytom-mail mailing list
> > Pyt...@li...
> > https://lists.sourceforge.net/lists/listinfo/pytom-mail
>
>


-- 
Best
Kanika Khanna
Graduate Student, Biological Sciences Department
University of California, San Diego

Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

[Thomas H. <th...@gm...>]

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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Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

[Dustin M. <dus...@gm...>]

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.
>> 
>> 
>> 
>> 
> -------------- next part --------------
> An HTML attachment was scrubbed...
> 
> ------------------------------
> 
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
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> ------------------------------
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> https://lists.sourceforge.net/lists/listinfo/pytom-mail
> 
> 
> End of Pytom-mail Digest, Vol 97, Issue 1
> *****************************************

Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

[Kanika K. <kk...@uc...>]

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.
>
>
>
>

Re: [Pytom-mail] FRMAlignment - New

[Dustin M. <dus...@gm...>]

Hi Ben,

Yes, the resolution is past Nyquist, it’s strange. What’s more is that the FSC itself is much lower if I calculate it directly; ~6nm which is more reasonable. The average also has some kind of weird artifact appearance, and the output FSC volumes look like the expected result. The pixel size is set correctly. Here’s the end of the job file:

<Reference FSCFilter="" File=“denovo_ref.bin8.em" PreWedge="" Weighting=""/>
<Mask Binning="1" Filename="initial_mask.bin8.em" isSphere="True"/>
<SampleInformation ParticleDiameter="700.0" PixelSize="20.832"/>

I think you’re right about it not being the wedge. I removed the wedge and got the same result as well as looking at the aligned wedge volumes and they are not in alignment. I also tried setting a cutoff radius of the wedge and same result.

Thanks for your suggestions.

Dustin


> On Feb 20, 2016, at 4:56 PM, Benjamin Himes <him...@gm...> wrote:
> 
> Hi Dustin,
> 
> If your pixel size is 2nm as you have stated, your Nyquist limit is 4nm, and the returned resolution is 4.04 nm - It probably has to do with this more so than the wedge masking, is your pixel size entered correctly? Even if the particles have been aligned falsely to have their missing wedge coincide, this shouldn't inflate the FSC because it is a normalized metric.
> 
> -Ben H.
> 
> *************************************
> Benjamin Himes
> Department of Structural Biology
> University of Pittsburgh School of Medicine
> 2050 Biomedical Science Tower 3 (BST3).
> 3501 5th Ave, Pittsburgh, PA 15260
> 
> (412) 648-7262 (Office)
> (412)648-8998 (Lab fax)
> *************************************
> 
> No trees were killed to send this message, but
> a large number of electrons were terribly inconvenienced.
> 
> It is an abiding passion of human beings to attempt to read and re-view history as an orderly progression of events running according to a well-coordinated and rational script. Don't be fooled.
> 
> 
> On Sat, Feb 20, 2016 at 3:04 PM, Dustin Morado <dus...@gm...> wrote:
> Ok I’ll try setting the missing wedge to empty (0,0?). I am pretty sure my wedge info is correct. Here is a single particle from the list:
> 
> <Particle Filename="Particles/tomogram_00067_000014.em">
>   <Rotation Paradigm="ZXZ" X="159.572727907" Z1="357.684564976" Z2="266.804752529"/>
>   <Shift X="-4.54808395912" Y="-5.45043039396" Z="-1.90781399571"/>
>   <PickPosition Origin="../../TOMOS/tomogram_00067.mrc" X="220.0" Y=“554.0" Z="406.0"/>
>   <Wedge Type="SingleTiltWedge">
>     <SingleTiltWedge Angle1="30.0" Angle2="30.0" CutoffRadius="0.0" Smooth="0.0">
>       <TiltAxisRotation Z1="0.0" Z2="0.0" X="0.0"/>
>     </SingleTiltWedge>
>   </Wedge>
>   <Score RemoveAutocorr="False" Type="FRMScore" Value="0.301624138979">
>     <PeakPrior Filename="" Radius="0.0" Smooth="-1.0"/>
>   </Score>
>   <Class Name="1"/>
> </Particle>
> 
> and the data was collected from -60, 60 at 3 degrees increments.
> 
> —
> Cheers,
> Dustin
> 
> 
> > On Feb 20, 2016, at 4:44 AM, Yuxiang Chen <che...@gm...> wrote:
> >
> > Hi Dustin,
> >
> > that means for some reason the determined resolution (according to the set FSC value) is too high, which cannot be true.
> > Most likely the particles were aligned to the missing wedges. Please check the wedge settings in your particles.
> > If the wedges are set correctly and the problem still occurs, I'd suggest to set the wedges to empty to avoid aligning towards missing wedge direction.
> >
> > Cheers,
> > Yuxiang
> >
> >
> >
> > On Sat, Feb 20, 2016 at 2:47 AM, Dustin Morado <dus...@gm...> wrote:
> > Hi all,
> >
> > I keep getting the following termination to my FRM jobs
> >
> > current resolution 40.4014545455 1.03125
> > New frequency too high. Terminate!
> >
> > My Job field has the following:
> > <FRMJob PeakOffset="4" BandwidthRange="[4, 32]" Frequency="6" Destination="." MaxIterations="10" RScore="False" WeightedAverage="False" BFactor="None" AdaptiveResolution="0.1" FSC="0.5”>
> >
> > My particles are 64x64x64 with a 2nm pixel size so for some reason even if I set the initial frequency to an incredibly low resolution I still get this same abort. I have tried changing the frequency and the bw_range, but the only way I can get it to run for more than one iteration is to set the FSC to a very high value ~0.75+.
> >
> > Any suggestions?
> >
> > —
> > Cheers,
> > Dustin
> >
> >
> >
> 
> 
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
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> 

Re: [Pytom-mail] FRMAlignment - New

[Benjamin H. <him...@gm...>]

Hi Dustin,

If your pixel size is 2nm as you have stated, your Nyquist limit is 4nm,
and the returned resolution is 4.04 nm - It probably has to do with this
more so than the wedge masking, is your pixel size entered correctly? Even
if the particles have been aligned falsely to have their missing wedge
coincide, this shouldn't inflate the FSC because it is a normalized metric.

-Ben H.

*************************************
Benjamin Himes
Department of Structural Biology
University of Pittsburgh School of Medicine
2050 Biomedical Science Tower 3 (BST3).
3501 5th Ave, Pittsburgh, PA 15260

*(412) 648-7262 *(Office)
*(412)648-8998* (Lab fax)
*************************************

No trees were killed to send this message, but
a large number of electrons were terribly inconvenienced.

It is an abiding passion of human beings to attempt to read and re-view
history as an orderly progression of events running according to a
well-coordinated and rational script. Don't be fooled.


On Sat, Feb 20, 2016 at 3:04 PM, Dustin Morado <dus...@gm...>
wrote:

> Ok I’ll try setting the missing wedge to empty (0,0?). I am pretty sure my
> wedge info is correct. Here is a single particle from the list:
>
> <Particle Filename="Particles/tomogram_00067_000014.em">
>   <Rotation Paradigm="ZXZ" X="159.572727907" Z1="357.684564976"
> Z2="266.804752529"/>
>   <Shift X="-4.54808395912" Y="-5.45043039396" Z="-1.90781399571"/>
>   <PickPosition Origin="../../TOMOS/tomogram_00067.mrc" X="220.0"
> Y=“554.0" Z="406.0"/>
>   <Wedge Type="SingleTiltWedge">
>     <SingleTiltWedge Angle1="30.0" Angle2="30.0" CutoffRadius="0.0"
> Smooth="0.0">
>       <TiltAxisRotation Z1="0.0" Z2="0.0" X="0.0"/>
>     </SingleTiltWedge>
>   </Wedge>
>   <Score RemoveAutocorr="False" Type="FRMScore" Value="0.301624138979">
>     <PeakPrior Filename="" Radius="0.0" Smooth="-1.0"/>
>   </Score>
>   <Class Name="1"/>
> </Particle>
>
> and the data was collected from -60, 60 at 3 degrees increments.
>
> —
> Cheers,
> Dustin
>
>
> > On Feb 20, 2016, at 4:44 AM, Yuxiang Chen <che...@gm...> wrote:
> >
> > Hi Dustin,
> >
> > that means for some reason the determined resolution (according to the
> set FSC value) is too high, which cannot be true.
> > Most likely the particles were aligned to the missing wedges. Please
> check the wedge settings in your particles.
> > If the wedges are set correctly and the problem still occurs, I'd
> suggest to set the wedges to empty to avoid aligning towards missing wedge
> direction.
> >
> > Cheers,
> > Yuxiang
> >
> >
> >
> > On Sat, Feb 20, 2016 at 2:47 AM, Dustin Morado <dus...@gm...>
> wrote:
> > Hi all,
> >
> > I keep getting the following termination to my FRM jobs
> >
> > current resolution 40.4014545455 1.03125
> > New frequency too high. Terminate!
> >
> > My Job field has the following:
> > <FRMJob PeakOffset="4" BandwidthRange="[4, 32]" Frequency="6"
> Destination="." MaxIterations="10" RScore="False" WeightedAverage="False"
> BFactor="None" AdaptiveResolution="0.1" FSC="0.5”>
> >
> > My particles are 64x64x64 with a 2nm pixel size so for some reason even
> if I set the initial frequency to an incredibly low resolution I still get
> this same abort. I have tried changing the frequency and the bw_range, but
> the only way I can get it to run for more than one iteration is to set the
> FSC to a very high value ~0.75+.
> >
> > Any suggestions?
> >
> > —
> > Cheers,
> > Dustin
> >
> >
> >
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>

Re: [Pytom-mail] FRMAlignment - New

[Dustin M. <dus...@gm...>]

Ok I’ll try setting the missing wedge to empty (0,0?). I am pretty sure my wedge info is correct. Here is a single particle from the list:

<Particle Filename="Particles/tomogram_00067_000014.em">
  <Rotation Paradigm="ZXZ" X="159.572727907" Z1="357.684564976" Z2="266.804752529"/>
  <Shift X="-4.54808395912" Y="-5.45043039396" Z="-1.90781399571"/>
  <PickPosition Origin="../../TOMOS/tomogram_00067.mrc" X="220.0" Y=“554.0" Z="406.0"/>
  <Wedge Type="SingleTiltWedge">
    <SingleTiltWedge Angle1="30.0" Angle2="30.0" CutoffRadius="0.0" Smooth="0.0">
      <TiltAxisRotation Z1="0.0" Z2="0.0" X="0.0"/>
    </SingleTiltWedge>
  </Wedge>
  <Score RemoveAutocorr="False" Type="FRMScore" Value="0.301624138979">
    <PeakPrior Filename="" Radius="0.0" Smooth="-1.0"/>
  </Score>
  <Class Name="1"/>
</Particle>

and the data was collected from -60, 60 at 3 degrees increments.

—
Cheers,
Dustin


> On Feb 20, 2016, at 4:44 AM, Yuxiang Chen <che...@gm...> wrote:
> 
> Hi Dustin,
> 
> that means for some reason the determined resolution (according to the set FSC value) is too high, which cannot be true.
> Most likely the particles were aligned to the missing wedges. Please check the wedge settings in your particles.
> If the wedges are set correctly and the problem still occurs, I'd suggest to set the wedges to empty to avoid aligning towards missing wedge direction.
> 
> Cheers,
> Yuxiang
> 
> 
> 
> On Sat, Feb 20, 2016 at 2:47 AM, Dustin Morado <dus...@gm...> wrote:
> Hi all,
> 
> I keep getting the following termination to my FRM jobs
> 
> current resolution 40.4014545455 1.03125
> New frequency too high. Terminate!
> 
> My Job field has the following:
> <FRMJob PeakOffset="4" BandwidthRange="[4, 32]" Frequency="6" Destination="." MaxIterations="10" RScore="False" WeightedAverage="False" BFactor="None" AdaptiveResolution="0.1" FSC="0.5”>
> 
> My particles are 64x64x64 with a 2nm pixel size so for some reason even if I set the initial frequency to an incredibly low resolution I still get this same abort. I have tried changing the frequency and the bw_range, but the only way I can get it to run for more than one iteration is to set the FSC to a very high value ~0.75+.
> 
> Any suggestions?
> 
> —
> Cheers,
> Dustin
> 
> 
> 

Re: [Pytom-mail] FRMAlignment - New

[Yuxiang C. <che...@gm...>]

Hi Dustin,

that means for some reason the determined resolution (according to the set
FSC value) is too high, which cannot be true.
Most likely the particles were aligned to the missing wedges. Please check
the wedge settings in your particles.
If the wedges are set correctly and the problem still occurs, I'd suggest
to set the wedges to empty to avoid aligning towards missing wedge
direction.

Cheers,
Yuxiang



On Sat, Feb 20, 2016 at 2:47 AM, Dustin Morado <dus...@gm...>
wrote:

> Hi all,
>
> I keep getting the following termination to my FRM jobs
>
> current resolution 40.4014545455 1.03125
> New frequency too high. Terminate!
>
> My Job field has the following:
> <FRMJob PeakOffset="4" BandwidthRange="[4, 32]" Frequency="6"
> Destination="." MaxIterations="10" RScore="False" WeightedAverage="False"
> BFactor="None" AdaptiveResolution="0.1" FSC="0.5”>
>
> My particles are 64x64x64 with a 2nm pixel size so for some reason even if
> I set the initial frequency to an incredibly low resolution I still get
> this same abort. I have tried changing the frequency and the bw_range, but
> the only way I can get it to run for more than one iteration is to set the
> FSC to a very high value ~0.75+.
>
> Any suggestions?
>
> —
> Cheers,
> Dustin
>
>
>

[Pytom-mail] FRMAlignment - New

[Dustin M. <dus...@gm...>]

Hi all,

I keep getting the following termination to my FRM jobs 

current resolution 40.4014545455 1.03125
New frequency too high. Terminate!

My Job field has the following:
<FRMJob PeakOffset="4" BandwidthRange="[4, 32]" Frequency="6" Destination="." MaxIterations="10" RScore="False" WeightedAverage="False" BFactor="None" AdaptiveResolution="0.1" FSC="0.5”>

My particles are 64x64x64 with a 2nm pixel size so for some reason even if I set the initial frequency to an incredibly low resolution I still get this same abort. I have tried changing the frequency and the bw_range, but the only way I can get it to run for more than one iteration is to set the FSC to a very high value ~0.75+. 

Any suggestions?

—
Cheers,
Dustin

Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

[Thomas H. <th...@gm...>]

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... <mailto:pyt...@li...> wrote:
>> 
>> As list administrator, your authorization is requested for the
>> following mailing list posting:
>> 
>>    List:    Pyt...@li... <mailto:Pyt...@li...>
>>    From:    kha...@gm... <mailto: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 <https://lists.sourceforge.net/lists/admindb/pytom-mail>
>> 
>> to approve or deny the request.
>> 
>> From: Kanika Khanna <kha...@gm... <mailto:kha...@gm...>>
>> Subject: Particle extraction and pdb2em
>> Date: February 18, 2016 at 1:31:48 PM PST
>> To: pyt...@li... <mailto: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... <mailto: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.
>> 
> 

Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

[Kanika K. <kk...@uc...>]

Thank you Thomas!

On Thu, Feb 18, 2016 at 2:31 PM, Thomas Hrabe <th...@gm...> wrote:

> Thank you.
> I was able to fix a logical bug in the conversion script.
>
> Attached are your files. The bug will be fixed in the next release.
> I attached the fixed pytom.basic.files.py , so if you need it before,
> please use that one.
>
> Best,
> Thomas
>
>
>
>
>
>
>
>
> pdb2em.py -p 3uzo.pdb -s 4 -v 50 -o 3uzo.em
> pdb2em.py -p 3uzo.pdb -s 4 -v 50 -c A -o 3uzoA.em
> pdb2em.py -p 3uzo.pdb -s 4 -v 50 -c B -o chainB.em
>
>
> On Feb 18, 2016, at 2:19 PM, Kanika Khanna <kk...@uc...> wrote:
>
> Sure!
>
> The PDB ID I am using is 3UZO
>
> On Thu, Feb 18, 2016 at 2:16 PM, Thomas Hrabe <th...@gm...> wrote:
>
>> Can you please send me the PDB id you use?
>> Maybe we found bug worth fixing… :)
>> Thomas
>>
>> On Feb 18, 2016, at 2:09 PM, Kanika Khanna <kk...@uc...> wrote:
>>
>> Hello,
>>
>> 1. No, I am not specifying the chain.
>>
>> On Thu, Feb 18, 2016 at 2:04 PM, Thomas Hrabe <th...@gm...> wrote:
>>
>>> Hi Kanika,
>>>
>>> 1. are you specifying the chain you want, too?
>>> 2. Score and angle will after localization. These are the result files
>>> with the essential information.
>>>
>>> Best,
>>> Thomas
>>>
>>>
>>> On Feb 18, 2016, at 2:01 PM, Kanika Khanna <kk...@uc...> wrote:
>>>
>>> Thank you Thomas!
>>>
>>> 1. Yes, I have downloaded the pdb format only. I tried different pdb
>>> files and I get the same error all the time.
>>>
>>> 2. Is there a way to generate scores.em/angles.em file from Pytom?
>>>
>>> On Thu, 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.
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>
>

Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

[Thomas H. <th...@gm...>]

Thank you.
I was able to fix a logical bug in the conversion script.

Attached are your files. The bug will be fixed in the next release.
I attached the fixed pytom.basic.files.py , so if you need it before, please use that one. 

Best,
Thomas





pdb2em.py -p 3uzo.pdb -s 4 -v 50 -o 3uzo.em
pdb2em.py -p 3uzo.pdb -s 4 -v 50 -c A -o 3uzoA.em
pdb2em.py -p 3uzo.pdb -s 4 -v 50 -c B -o chainB.em


> On Feb 18, 2016, at 2:19 PM, Kanika Khanna <kk...@uc...> wrote:
> 
> Sure!
> 
> The PDB ID I am using is 3UZO
> 
> On Thu, Feb 18, 2016 at 2:16 PM, Thomas Hrabe <th...@gm... <mailto:th...@gm...>> wrote:
> Can you please send me the PDB id you use? 
> Maybe we found bug worth fixing… :)  
> Thomas
> 
>> On Feb 18, 2016, at 2:09 PM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote:
>> 
>> Hello,
>> 
>> 1. No, I am not specifying the chain. 
>> 
>> On Thu, Feb 18, 2016 at 2:04 PM, Thomas Hrabe <th...@gm... <mailto:th...@gm...>> wrote:
>> Hi Kanika,
>> 
>> 1. are you specifying the chain you want, too?
>> 2. Score and angle will after localization. These are the result files with the essential information.
>> 
>> Best,
>> Thomas
>> 
>> 
>>> On Feb 18, 2016, at 2:01 PM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote:
>>> 
>>> Thank you Thomas!
>>> 
>>> 1. Yes, I have downloaded the pdb format only. I tried different pdb files and I get the same error all the time.
>>> 
>>> 2. Is there a way to generate scores.em/angles.em file from Pytom?
>>> 
>>> On Thu, Feb 18, 2016 at 1:47 PM, Thomas Hrabe <th...@gm... <mailto: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... <mailto:pyt...@li...> wrote:
>>>> 
>>>> As list administrator, your authorization is requested for the
>>>> following mailing list posting:
>>>> 
>>>>    List:    Pyt...@li... <mailto:Pyt...@li...>
>>>>    From:    kha...@gm... <mailto: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 <https://lists.sourceforge.net/lists/admindb/pytom-mail>
>>>> 
>>>> to approve or deny the request.
>>>> 
>>>> From: Kanika Khanna <kha...@gm... <mailto:kha...@gm...>>
>>>> Subject: Particle extraction and pdb2em
>>>> Date: February 18, 2016 at 1:31:48 PM PST
>>>> To: pyt...@li... <mailto: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... <mailto: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.
>>>> 
>>> 
>>> 
>> 
>> 
> 
> 

[Pytom-mail] Particle extraction and pdb2em

[Kanika K. <kha...@gm...>]

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

[Pytom-mail] Particle extraction

[Kanika K. <kk...@uc...>]

Hello

I am new to Pytom and had a question as to how to generate the files
"scores.em" and "angles.em" for extraction of particles. Also, how the
localization results can be viewed?

Thanks

[Pytom-mail] Extraction of Particles

[Kanika K. <kha...@gm...>]

Hello

I am new to Pytom and had a question as to how to generate the files
"scores.em" and "angles.em" for extraction of particles. Also, how the
localization results can be viewed?

-- 
Best
Kanika Khanna
Graduate Student, Biological Sciences Department
University of California, San Diego

[Pytom-mail] Fwd: error on the first attempt at tutorial

[Villa, E. <ev...@uc...>]

hi all,  

We’re trying pytom for the first time and we seem to have issues. First we pulled the master branch, and now the devel branch, and we seem to have issues.  Can you please help?  We are following the website/tutorial instructions. 

Cheers, 
Elizabeth 




PyTom v0.97

This license affects the software package PyTom and all the herein distributed source / data files.
Authors: 
Thomas Hrabe
Yuxiang Chen
Friedrich Foerster

Copyright (c) 2008-2016
Max-Planck-Institute for Biochemistry
Dept. Molecular Structural Biology
82152 Martinsried, Germany
http://www.pytom.org

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

The complete license can be obtained from 
http://www.gnu.org/licenses/gpl-3.0.html.

sys.version_info(major=2, minor=7, micro=5, releaselevel='final', serial=0)
option --tiltSeriesPath not recognized
RibosFromLysate/reconstructTomo> 




> Begin forwarded message:
> 
> From: Elizabeth Villa <ev...@uc...>
> Subject: Re: error on the first attempt at tutorial
> Date: February 17, 2016 at 5:16:39 PM PST
> To: Thomas Hrabe <th...@sb...>
> Cc: Ittipat Meewan <im...@uc...>
> 
> Hmm.. I just pulled it from the git repository..  Will email the pytom list in the future.. 
> 
> thanks! 
> E
> 
> 
> 
>> On Feb 17, 2016, at 5:06 PM, Thomas Hrabe <th...@sb...> wrote:
>> 
>> Hi E,
>> 
>> haven’t played with the reconstruction before for a while.
>> Seems there’s a unset parameter. Obvious what it does, but do we have a different version running? In my release I find the line in row 178. The file is attached.
>> 
>> Please go through the mailing list next time, that’s the best way to get feedback from either of us, including Yuxiang and the whole pytom community (sometimes :) ).
>> 
>> My file is attached, or you can download the development branch from the GIT repository on sourceforge.
>> 
>> Thomas
>> 
>> 
>> 
>>> On Feb 17, 2016, at 4:23 PM, Villa, Elizabeth <ev...@uc...> wrote:
>>> 
>>> hi T, 
>>> 
>>> We just installed pytom and downloaded the tutorial. In the first attempt at reconstructing the tomo, I get:
>>> 
>>> The complete license can be obtained from 
>>> http://www.gnu.org/licenses/gpl-3.0.html.
>>> 
>>> Tilt Series: ../projections/tomo01_sorted 1-41
>>> Index of Reference Projection21
>>> Marker Filename:../projections/markfile_temp.mark, Index of Reference Marker:1
>>> Handflip:False
>>> Projection Targets: ./alignedProjections/tomo01
>>> FineAlignmentFile: None
>>> Binning Factor of Projections: 4, lowpass filter (in Ny): 0.5
>>> Name of Reconstruction Volume: tomogram.em of Filetype: em
>>> Reconstruction size: ['512', '512', '128']
>>> Reconstruction center: ['0', '0', '0']
>>> Traceback (most recent call last):
>>>   File "/usr/local/pytom/bin/reconstructTomogram.py", line 138, in <module>
>>>     print "write only projections out: "+str(onlyWeightedProjections)
>>> NameError: name 'onlyWeightedProjections' is not defined
>>> [evilla@pordoi reconstructTomo]$ 
>>> 
>>> 
>>> The weird thing is that onlyWeightedProjections  is not a flag in the script, so it must have been a default option that got dropped?  
>>> 
>>> Should we contact Frido’s group about this? 
>>> 
>>> Thanks! 
>>> E
>>> 
>>> 
>>> 
>>> --
>>> Elizabeth Villa
>>> Department of Chemistry and Biochemistry
>>> University of California San Diego 
>>> 
>>> w: villalab.ucsd.edu
>>> v:  +1 (858) 246-1843
>>> f: +1 (858) 534-4864
>>> 
>>> 
>>> 
>> 
>> <reconstructTomogram.py>
> 
> --
> Elizabeth Villa
> Department of Chemistry and Biochemistry
> University of California San Diego 
> 
> w:	villalab.ucsd.edu
> v: 	+1 (858) 246-1843
> f:	+1 (858) 534-4864
> 
> 
> 

--
Elizabeth Villa
Department of Chemistry and Biochemistry
University of California San Diego 

w:	villalab.ucsd.edu
v: 	+1 (858) 246-1843
f:	+1 (858) 534-4864

Re: [Pytom-mail] Error creating alignment job in web server

[Thomas H. <th...@gm...>]

Dustin,

you can do the following:

pytom/frontend/serverpages/createAlignmentJob.py 

add the default parameters before line 145

    if 'adapt' in parameters:
        fscCriterion=0.5
        resOffset = 0.1
        angleFactor = 0.5
        adaptive = parameters['adapt'] == 'ON'

Let me know if it fixed the issue.

Thomas


> On Feb 16, 2016, at 1:25 PM, Dustin Morado <dus...@gm...> wrote:
> 
> Thomas,
> 
> Sorry for the delay. I made the hot fix and now get this error:
> 
> Error: local variable 'fscCriterion' referenced before assignment
> 
> Dustin
> 
>> On Feb 3, 2016, at 1:23 PM, Thomas Hrabe <th...@gm...> wrote:
>> 
>> Dustin,
>> 
>> as a hotfix you can try replacing line 126 in pytom.frontend.createAlignmentJob.py
>> with this line:
>> 
>> angles = LocalSampling(shells=shells,increment=startIncrement)
>> 
>> Please try and let me know if it worked. I will test it here too and update in the next release.
>> 
>> Thomas
>> 
>> 
>>> On Feb 3, 2016, at 10:43 AM, Thomas Hrabe <th...@gm...> wrote:
>>> 
>>> Hi Dustin,
>>> 
>>> thank you for the bug report. 
>>> The web-interface was not touched in recently and my first guess is that a refactoring was not propagated into that part.
>>> I’ll check.
>>> 
>>> You are right about the interface for non experts, but since the CLI works alright please show your lab-mates how to use it meanwhile.
>>> 
>>> Thanks,
>>> Thomas
>>> 
>>> 
>>>> On Feb 3, 2016, at 8:29 AM, Dustin Morado <dus...@gm...> wrote:
>>>> 
>>>> Hi all,
>>>> 
>>>> In case it is of any use, here is also the output from pytomServer. It’s interesting the only error shows up when it was run on Firefox and there doesn’t appear to be any feedback from the errors on Chrome and Safari.
>>>> 
>>>> and I just noticed that it’s calling an older version of pytom. I have pytom 0.963 in /opt/pytom, and pytom 0.97 in /opt/pytom_0.97, but haven’t had any other problems running jobs from the command line with this setup.
>>>> 
>>>> —
>>>> Dustin
>>>> 
>>>> <pytomServer.out>
>>>> 
>>>>> Message: 1
>>>>> Date: Wed, 3 Feb 2016 10:12:08 -0600
>>>>> From: Dustin Morado <dus...@gm...>
>>>>> Subject: [Pytom-mail] Error creating alignment job in web server
>>>>> To: pyt...@li...
>>>>> Message-ID: <108...@gm...>
>>>>> Content-Type: text/plain; charset=utf-8
>>>>> 
>>>>> Hi al,
>>>>> 
>>>>> I get the following error when trying to create an alignment job from the web server front end.
>>>>> I am using pytom 0.97 and the create job button is green in the interface.
>>>>> 
>>>>> invalidStateError: Failed to execute 'overrideMimeType' on 'XMLHttpRequest?: 
>>>>> Mime Type cannot be overridden when the state is LOADING or DONE.
>>>>> 
>>>>> I?m running the web server on a remote station and accessing it through port forwarding to my laptop.
>>>>> I?m using Google Chrome.
>>>>> 
>>>>> If I use Safari in the same manner I get this error instead:
>>>>> Error: InvalidStateError: DOM Exception 11
>>>>> 
>>>>> If I use Firefox I get this error:
>>>>> Error: __init__() got an unexpected keyword argument ?shellIncrement'
>>>>> 
>>>>> I?m OK setting up jobs myself through the command line, but GUI access would be preferred for the less computer savvy in my lab.
>>>>> 
>>>>> Thanks for the help!
>>>>> 
>>>>> ?
>>>>> Cheers,
>>>>> Dustin Morado
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>> Monitor end-to-end web transactions and take corrective actions now
>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________
>>>> Pytom-mail mailing list
>>>> Pyt...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>>> 
>> 
> 

Re: [Pytom-mail] ParticleList.addRotation and addShift error

[Thomas H. <th...@gm...>]

Hi Dustin,

Hotfix:
delete the object= and class_or_type_or_tuple  parameter names in pytom.basic.structures and the respective lines.

Even though the parameters are named as they were used in the code, the function does not keyword arguments.
Fails on my python 2.7.10 installation.

I am adding that to the next release.

Thomas

> On Feb 16, 2016, at 5:16 PM, Dustin Morado <dus...@gm...> wrote:
> 
> Hi all,
> 
> I get the following error when trying to use the addRotation and addShift methods in the ParticleList class:
> 
> In [13]: myPl.addRotation(myRot)
> ---------------------------------------------------------------------------
> TypeError                                 Traceback (most recent call last)
> <ipython-input-13-80fb14b533f5> in <module>()
> ----> 1 myPl.addRotation(myRot)
> 
> /opt/pytom/basic/structures.py in addRotation(self, rot)
>   3076         @author: FF
>   3077         """
> -> 3078         assert isinstance(object=rot, class_or_type_or_tuple=Rotation), "addRotation: rot must be Rotation!"
>   3079         for part in self._particleList:
>   3080             trot = part.getRotation()
> 
> TypeError: isinstance() takes no keyword arguments
> 
> In [14]: myPl.addShift(myShift)
> ---------------------------------------------------------------------------
> TypeError                                 Traceback (most recent call last)
> <ipython-input-14-7e01fc0362f4> in <module>()
> ----> 1 myPl.addShift(myShift)
> 
> /opt/pytom/basic/structures.py in addShift(self, translation)
>   3090         @author: FF
>   3091         """
> -> 3092         assert isinstance(object=translation, class_or_type_or_tuple=Shift), "addShift: rot must be Rotation!"
>   3093         for part in self._particleList:
>   3094             ttrans = part.getShift()
> 
> TypeError: isinstance() takes no keyword arguments
> 
> —
> Cheers,
> Dustin
> <ipytom.err>------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
> Pytom-mail mailing list
> Pyt...@li...
> https://lists.sourceforge.net/lists/listinfo/pytom-mail

[Pytom-mail] ParticleList.addRotation and addShift error

[Dustin M. <dus...@gm...>]

Hi all,

I get the following error when trying to use the addRotation and addShift methods in the ParticleList class:

In [13]: myPl.addRotation(myRot)
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-13-80fb14b533f5> in <module>()
----> 1 myPl.addRotation(myRot)

/opt/pytom/basic/structures.py in addRotation(self, rot)
   3076         @author: FF
   3077         """
-> 3078         assert isinstance(object=rot, class_or_type_or_tuple=Rotation), "addRotation: rot must be Rotation!"
   3079         for part in self._particleList:
   3080             trot = part.getRotation()

TypeError: isinstance() takes no keyword arguments

In [14]: myPl.addShift(myShift)
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-14-7e01fc0362f4> in <module>()
----> 1 myPl.addShift(myShift)

/opt/pytom/basic/structures.py in addShift(self, translation)
   3090         @author: FF
   3091         """
-> 3092         assert isinstance(object=translation, class_or_type_or_tuple=Shift), "addShift: rot must be Rotation!"
   3093         for part in self._particleList:
   3094             ttrans = part.getShift()

TypeError: isinstance() takes no keyword arguments

—
Cheers,
Dustin

Re: [Pytom-mail] Error creating alignment job in web server

[Dustin M. <dus...@gm...>]

Thomas,

Sorry for the delay. I made the hot fix and now get this error:

Error: local variable 'fscCriterion' referenced before assignment

Dustin

> On Feb 3, 2016, at 1:23 PM, Thomas Hrabe <th...@gm...> wrote:
> 
> Dustin,
> 
> as a hotfix you can try replacing line 126 in pytom.frontend.createAlignmentJob.py
> with this line:
> 
> angles = LocalSampling(shells=shells,increment=startIncrement)
> 
> Please try and let me know if it worked. I will test it here too and update in the next release.
> 
> Thomas
> 
> 
>> On Feb 3, 2016, at 10:43 AM, Thomas Hrabe <th...@gm...> wrote:
>> 
>> Hi Dustin,
>> 
>> thank you for the bug report. 
>> The web-interface was not touched in recently and my first guess is that a refactoring was not propagated into that part.
>> I’ll check.
>> 
>> You are right about the interface for non experts, but since the CLI works alright please show your lab-mates how to use it meanwhile.
>> 
>> Thanks,
>> Thomas
>> 
>> 
>>> On Feb 3, 2016, at 8:29 AM, Dustin Morado <dus...@gm...> wrote:
>>> 
>>> Hi all,
>>> 
>>> In case it is of any use, here is also the output from pytomServer. It’s interesting the only error shows up when it was run on Firefox and there doesn’t appear to be any feedback from the errors on Chrome and Safari.
>>> 
>>> and I just noticed that it’s calling an older version of pytom. I have pytom 0.963 in /opt/pytom, and pytom 0.97 in /opt/pytom_0.97, but haven’t had any other problems running jobs from the command line with this setup.
>>> 
>>> —
>>> Dustin
>>> 
>>> <pytomServer.out>
>>> 
>>>> Message: 1
>>>> Date: Wed, 3 Feb 2016 10:12:08 -0600
>>>> From: Dustin Morado <dus...@gm...>
>>>> Subject: [Pytom-mail] Error creating alignment job in web server
>>>> To: pyt...@li...
>>>> Message-ID: <108...@gm...>
>>>> Content-Type: text/plain; charset=utf-8
>>>> 
>>>> Hi al,
>>>> 
>>>> I get the following error when trying to create an alignment job from the web server front end.
>>>> I am using pytom 0.97 and the create job button is green in the interface.
>>>> 
>>>> invalidStateError: Failed to execute 'overrideMimeType' on 'XMLHttpRequest?: 
>>>> Mime Type cannot be overridden when the state is LOADING or DONE.
>>>> 
>>>> I?m running the web server on a remote station and accessing it through port forwarding to my laptop.
>>>> I?m using Google Chrome.
>>>> 
>>>> If I use Safari in the same manner I get this error instead:
>>>> Error: InvalidStateError: DOM Exception 11
>>>> 
>>>> If I use Firefox I get this error:
>>>> Error: __init__() got an unexpected keyword argument ?shellIncrement'
>>>> 
>>>> I?m OK setting up jobs myself through the command line, but GUI access would be preferred for the less computer savvy in my lab.
>>>> 
>>>> Thanks for the help!
>>>> 
>>>> ?
>>>> Cheers,
>>>> Dustin Morado
>>> 
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________
>>> Pytom-mail mailing list
>>> Pyt...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>> 
> 

Re: [Pytom-mail] Error creating alignment job in web server

[Thomas H. <th...@gm...>]

Dustin,

as a hotfix you can try replacing line 126 in pytom.frontend.createAlignmentJob.py
with this line:

angles = LocalSampling(shells=shells,increment=startIncrement)

Please try and let me know if it worked. I will test it here too and update in the next release.

Thomas


> On Feb 3, 2016, at 10:43 AM, Thomas Hrabe <th...@gm...> wrote:
> 
> Hi Dustin,
> 
> thank you for the bug report. 
> The web-interface was not touched in recently and my first guess is that a refactoring was not propagated into that part.
> I’ll check.
> 
> You are right about the interface for non experts, but since the CLI works alright please show your lab-mates how to use it meanwhile.
> 
> Thanks,
> Thomas
> 
> 
>> On Feb 3, 2016, at 8:29 AM, Dustin Morado <dus...@gm...> wrote:
>> 
>> Hi all,
>> 
>> In case it is of any use, here is also the output from pytomServer. It’s interesting the only error shows up when it was run on Firefox and there doesn’t appear to be any feedback from the errors on Chrome and Safari.
>> 
>> and I just noticed that it’s calling an older version of pytom. I have pytom 0.963 in /opt/pytom, and pytom 0.97 in /opt/pytom_0.97, but haven’t had any other problems running jobs from the command line with this setup.
>> 
>> —
>> Dustin
>> 
>> <pytomServer.out>
>> 
>>> Message: 1
>>> Date: Wed, 3 Feb 2016 10:12:08 -0600
>>> From: Dustin Morado <dus...@gm...>
>>> Subject: [Pytom-mail] Error creating alignment job in web server
>>> To: pyt...@li...
>>> Message-ID: <108...@gm...>
>>> Content-Type: text/plain; charset=utf-8
>>> 
>>> Hi al,
>>> 
>>> I get the following error when trying to create an alignment job from the web server front end.
>>> I am using pytom 0.97 and the create job button is green in the interface.
>>> 
>>> invalidStateError: Failed to execute 'overrideMimeType' on 'XMLHttpRequest?: 
>>> Mime Type cannot be overridden when the state is LOADING or DONE.
>>> 
>>> I?m running the web server on a remote station and accessing it through port forwarding to my laptop.
>>> I?m using Google Chrome.
>>> 
>>> If I use Safari in the same manner I get this error instead:
>>> Error: InvalidStateError: DOM Exception 11
>>> 
>>> If I use Firefox I get this error:
>>> Error: __init__() got an unexpected keyword argument ?shellIncrement'
>>> 
>>> I?m OK setting up jobs myself through the command line, but GUI access would be preferred for the less computer savvy in my lab.
>>> 
>>> Thanks for the help!
>>> 
>>> ?
>>> Cheers,
>>> Dustin Morado
>> 
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________
>> Pytom-mail mailing list
>> Pyt...@li...
>> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>