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Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval
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From: Dustin M. <dus...@gm...> - 2016-02-23 01:38:51
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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 > ***************************************** |
