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
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Received on Tue Jul 05 2016 - 19:00:02 PDT
