Re: [IMP-dev] read_pdb in imp
One gets warnings like that when atoms are read from the PDB whose atom type (the 3rd entry on an ATOM line in the PDB file) is something non-standard or incorrect. They aren't necessarily worth worrying about, depending on what you want to do with the file.
We could, perhaps, provide the residue type and index in the error message which might make the message easier to deal with (Ben would know more). However, there is a tradeoff as the warnings in PDB reading are collapsed to only print out each warning once and files with an unknown atom type often have many of the same unknown atom type. So adding the residue index might results in lots and lots of warnings :-)
On Jun 29, 2012, at 7:53 PM, Khuri, Natalia wrote:
> Hi Ben and Daniel! > > Not sure who to direct this question, but I get the following warning when i try to read a myoglobin pdb file: > ========= > begin read_pdb: > WARNING Radius not found for type, default value is used "NP1" > ========== > Here is the Python code I am using: > > import IMP.atom > m= IMP.Model() > h= IMP.atom.read_pdb("1DWR.pdb",m) > > Is there a way to make the warning more descriptive? I do not know where to start looking for the atom in question. > Also, should I post the questions to the forum on-line instead of sending them to you directly? > > Thank you, > > Natalia Khuri > PhD Student, Graduate Group in Biophysics > Laboratory of Andrej Sali > UCSF MC 2552 > Byers Hall Room 503B > 1700 4th Street > San Francisco, CA 94158-2330, USA
Thanks, Daniel!
Ben: is it possible to save all warnings/errors in a .err file, so that users can decide if they are something to worry about or not?
Natalia Khuri PhD Student, Graduate Group in Biophysics Laboratory of Andrej Sali UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA ________________________________ From: Daniel Russel [drussel@gmail.com] on behalf of Daniel Russel [drussel@salilab.org] Sent: Friday, June 29, 2012 8:44 PM To: Khuri, Natalia Cc: List for IMP development Subject: Re: read_pdb in imp
One gets warnings like that when atoms are read from the PDB whose atom type (the 3rd entry on an ATOM line in the PDB file) is something non-standard or incorrect. They aren't necessarily worth worrying about, depending on what you want to do with the file.
We could, perhaps, provide the residue type and index in the error message which might make the message easier to deal with (Ben would know more). However, there is a tradeoff as the warnings in PDB reading are collapsed to only print out each warning once and files with an unknown atom type often have many of the same unknown atom type. So adding the residue index might results in lots and lots of warnings :-)
On Jun 29, 2012, at 7:53 PM, Khuri, Natalia wrote:
Hi Ben and Daniel!
Not sure who to direct this question, but I get the following warning when i try to read a myoglobin pdb file: ========= begin read_pdb: WARNING Radius not found for type, default value is used "NP1" ========== Here is the Python code I am using:
import IMP.atom m= IMP.Model() h= IMP.atom.read_pdb("1DWR.pdb",m)
Is there a way to make the warning more descriptive? I do not know where to start looking for the atom in question. Also, should I post the questions to the forum on-line instead of sending them to you directly?
Thank you,
Natalia Khuri PhD Student, Graduate Group in Biophysics Laboratory of Andrej Sali UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA
On 06/30/2012 09:11 AM, Khuri, Natalia wrote: > Ben: is it possible to save all warnings/errors in a .err file, so that > users can decide if they are something to worry about or not?
You can send the log output anywhere you want by using SetLogTarget. But as Daniel points out, we had to choose between flooding the logs with output when reading a PDB versus only warning once per atom type, and we chose the latter.
That said, the log message is unambiguous:
WARNING Radius not found for type, default value is used "NP1"
Radii are looked up based on their CHARMM atom types, which are defined in top_heav.lib (in the data/atom/ directory). By looking in top_heav.lib, you can see that NP1 is a heme nitrogen. But there are no van der Waals parameters defined for NP1 in par.lib in the NONB section, so IMP will use a default radius. Unless you're planning to do detailed electrostatic calculations involving heme groups (I wouldn't recommend IMP for this anyway) this is nothing to worry about.
Ben
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Ben Webb -
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Khuri, Natalia