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Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval
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From: Thomas H. <th...@gm...> - 2016-02-23 17:36:12
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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. 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