Re: [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py

From: Bilal Nizami <nizamibilal1064.gmail.com>
Date: Wed, 6 Jul 2016 14:37:19 +0200

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






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Received on Wed Jul 06 2016 - 06:00:06 PDT
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