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
>
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> 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*
>>>>
>>>>
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>>>>
>>>
>>>
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