Hi Bilal,
Thanks for sending these files. The bugs have been fixed in GitHub: https://github.com/Amber-MD/pymsmt/tree/release2 <https://github.com/Amber-MD/pymsmt/tree/release2>.
Kind regards,
Pengfei
> On Jul 6, 2016, at 8:37 AM, Bilal Nizami <nizamibilal1064.gmail.com> wrote:
>
> Hi Pengfei,
>
> Thanks!!, I will look into references 56-61.
>
> Kindly find the 3 attached PDB file, which has a Ca metal. These are the
> some PDBs failing with IndexError.
>
> I tried with exception handling, where I put the entire code of
> PdbSearcher.py inside the try-except block. It seems to work, i.e. program
> doesn't terminate if the cut off criteria is not met, and it move to next
> pdb file.
>
> As far as error in "cal.py" file is concerned, it happens only, if
> #8-Coordinated, 28 angles is found (when using cut off 3.0). The pdb file
> 966c is attached for this error.
>
> Kind Regards,
>
> 2016-07-06 3:30 GMT+02:00 Pengfei Li <ambermailpengfei.gmail.com>:
>
>> Hi Bilal,
>>
>> Thanks for your interest in PdbSearcher.py.
>>
>>> On Jul 4, 2016, at 4:39 AM, Bilal Nizami <nizamibilal1064.gmail.com>
>> wrote:
>>>
>>> Hello Amber users,
>>>
>>> I am using PdbSearcher.py from Ambertool16 to determine the Calcium
>>> environement that exist in all the mettaloproteins in a local copy of PDB
>>> databse (~1000000 pdbs).
>>>
>>> In 2010 paper (http://pubs.acs.org/doi/abs/10.1021/ct1002626) describing
>>> MCPB, Harding's Metal-Donor bond length is mentioned for few residues
>>> surrounding metal center. I am wondering which cut off to use, because
>> any
>>> of the
>>> residue could be present in the vicinity. Any suggestions?
>>>
>>
>> I am not the author of this paper so I am not very sure about this.
>> According to the paper, it seems references 56-61 in the original paper
>> could be helpful.
>>
>>> Secondly, I have noticed some errors with PdbSearcher.py
>>>
>>>
>>> For many metalloprotein containing the search metal (I tried with Zn, Ca
>>> and Mn), it throws following error
>>>
>>> *Traceback (most recent call last):*
>>> * File "/home/bnizami/amber16/bin/PdbSearcher.py", line 195, in
>> <module>*
>>> * geo, georms = det_geo(mccrds)*
>>> * File
>> "/home/bnizami/amber16/lib/python2.7/site-packages/msmtmol/cal.py",
>>> line 99, in det_geo*
>>> * metcrd = crds[0]*
>>> *IndexError: list index out of range *
>>>
>>>
>>> I looked up in the PdbSearcher.py source code, it seems that following
>>> condition fails for the PDB, that the metal is not within the cut off
>>> radius.
>>>
>>> *if (disij >= 0.1) and (disij <= radiusij) and (elmtj != 'H')*
>>>
>>>
>>> I think, this part could be written inside a try-except block to avoid
>> the
>>> program termination in case metal is found but cutoff criteria is failed.
>>> To further test, i tried cutoff values like 2.9 and 3 Angstrom by -c flag
>>> to PdbSearcher.py. Again, this worked for the some pdbs, but failed for
>>> some to get the geometry with the following error:
>>>
>>> Find metal center DDNXXY
>>> Traceback (most recent call last):
>>> File "/home/bnizami/amber16/bin/PdbSearcher.py", line 195, in <module>
>>> geo, georms = det_geo(mccrds)
>>> File "/home/bnizami/amber16/lib/python2.7/site-packages/msmtmol/cal.py",
>>> line 223, in det_geo
>>> angrms = round(angrms3, 3)
>>> UnboundLocalError: local variable 'angrms3' referenced before assignment
>>>
>>>
>>> In my opinion, the reason for this error is line line 223 in cal.py
>> 'angrms
>>> = round(angrms3, 3)', where probably 'angrms3' should be 'angrms'.
>> Because
>>> angrms3 is assigned value inside the condition "elif len(crds) == 5:
>>> #5-Coordinated, 10 angles", in case the condition is not met and
>> condition
>>> "elif len(crds) == 8: #8-Coordinated, 28 angles" at line 225 is
>> satisfied,
>>> which leads to referencing the unassigned angrms3 at line 223.
>>>
>>> Kind Regards,
>>>
>>
>> Can you send me some PDB files which meet these errors? I can help to do a
>> check.
>>
>> Kind regards,
>> Pengfei
>>
>>>
>>> --
>>> *Bilal Nizami*
>>> School of Health Sciences
>>> University of KwaZulu-Natal
>>> Durban
>>> 4000
>>> South Africa
>>>
>>> Linkedin: za.linkedin.com/pub/bilal-nizami/49/673/790/
>>> Email: 214573074.stu.ukzn.ac.za
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
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>>
>
>
>
> --
> *Bilal Nizami*
> School of Health Sciences
> University of KwaZulu-Natal
> Durban
> 4000
> South Africa
>
> Linkedin: za.linkedin.com/pub/bilal-nizami/49/673/790/
> Email: 214573074.stu.ukzn.ac.za
> <1caq.pdb><2oeo.pdb><pdb426d.ent><966c.pdb>_______________________________________________
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Received on Sat Jul 09 2016 - 15:00:03 PDT
