Re: [COOT] pdb file problem with duplicate amino acid

[Paul Emsley]

On 31/01/2017 20:09, Dale Tronrud wrote:

On 1/31/2017 11:51 AM, Paul Emsley wrote:

On 31/01/17 17:54, Edwin Pozharski wrote:

Whatever the rationale was, there is a structure in the PDB that has
alternate conformer of a residue listed with different residue type -
A is arginine and B is glutamine.  Coot fails to load the model
complaining in the command window

WARNING:: Error reading small-molecule cif "/home/epo/coot/foo.pdb"
There was an error reading /home/epo/coot/foo.pdb.
ERROR 42 READ: Duplicate sequence number and insertion code.
 LINE #1571
 ATOM   1666  N  BGLN B  93  24.448  28.340 -33.325  0.50
9.34   N

No Spacegroup found for this PDB file
There was a coordinates read error



https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1503=COOT===25056



   I think this is a poor solution.


We agree, I think, that it is not a good solution.


 Microheterogeneity is not a duplicate residue number.


Isn't it? My understanding is that using the same residue number for a different residue 
type is *is* how microheterogeneity is specified.



 Not any more so than the alternative
conformation that is also indicated with "alt loc" letters.


I don't follow this, but if you mean that to describe microheterogeneity by using an altloc 
is the Wrong Way, then I agree with you.


> Both come up quite often in the PDB,

One man's quite often is another man's very rarely.


and microheterogeneity probably should be put
in models more often than it currently is.


I don't doubt that you are right.


Many modelers simply don't
realize it is a possibility.


I agree.


Your users rarely going to know about the
need to put this option into their startup file.


Indeed, if Ed has to ask the list, then I need to reconsider how I arrange this 
problem/work-around. (Maybe mmdb2 (or coot?) no longer has the problem with atom selection 
in models that have duplicate sequence numbers).


Paul.

Re: [COOT] pdb file problem with duplicate amino acid

[Edwin Pozharski]

Thanks - sorry I should have searched the archives first.  As a suggestion,
could you alter the warning text to include the fix decription (i.e.
"include this in your .coot.py)?  This way users would know what to do
right away.

On Tue, Jan 31, 2017 at 2:51 PM, Paul Emsley 
wrote:

> On 31/01/17 17:54, Edwin Pozharski wrote:
>
> Whatever the rationale was, there is a structure in the PDB that has
> alternate conformer of a residue listed with different residue type - A is
> arginine and B is glutamine.  Coot fails to load the model complaining in
> the command window
>
> WARNING:: Error reading small-molecule cif "/home/epo/coot/foo.pdb"
>> There was an error reading /home/epo/coot/foo.pdb.
>> ERROR 42 READ: Duplicate sequence number and insertion code.
>>  LINE #1571
>>  ATOM   1666  N  BGLN B  93  24.448  28.340 -33.325  0.50
>> 9.34   N
>>
>> No Spacegroup found for this PDB file
>> There was a coordinates read error
>>
>
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1503=
> COOT===25056
>
> Paul.
>

Re: [COOT] pdb file problem with duplicate amino acid

[Dale Tronrud]

On 1/31/2017 11:51 AM, Paul Emsley wrote:
> On 31/01/17 17:54, Edwin Pozharski wrote:
>> Whatever the rationale was, there is a structure in the PDB that has
>> alternate conformer of a residue listed with different residue type -
>> A is arginine and B is glutamine.  Coot fails to load the model
>> complaining in the command window
>>
>> WARNING:: Error reading small-molecule cif "/home/epo/coot/foo.pdb"
>> There was an error reading /home/epo/coot/foo.pdb.
>> ERROR 42 READ: Duplicate sequence number and insertion code.
>>  LINE #1571
>>  ATOM   1666  N  BGLN B  93  24.448  28.340 -33.325  0.50 
>> 9.34   N 
>>
>> No Spacegroup found for this PDB file
>> There was a coordinates read error
>>
> 
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1503=COOT===25056
> 
> Paul.

   I think this is a poor solution.  Microheterogeneity is not a
duplicate residue number.  Not any more so than the alternative
conformation that is also indicated with "alt loc" letters.  Both come
up quite often in the PDB, and microheterogeneity probably should be put
in models more often than it currently is.  May modelers simply don't
realize it is a possibility.  Your users rarely going to know about the
need to put this option into their startup file.

Dale

Re: [COOT] pdb file problem with duplicate amino acid

[Dale Tronrud]

   This is an occurrence of microheterogeneity and it is not all that
uncommon.  See Crambin as a classic prototype.  Coot should be able to
handle this.

   The work-around you suggest creates a very different model.  Residue
93A lies between 93 and 94 so you are actually inserting an entire
residue into the chain.

Dale Tronrud

On 1/31/2017 9:54 AM, Edwin Pozharski wrote:
> Whatever the rationale was, there is a structure in the PDB that has
> alternate conformer of a residue listed with different residue type - A
> is arginine and B is glutamine.  Coot fails to load the model
> complaining in the command window
> 
> WARNING:: Error reading small-molecule cif "/home/epo/coot/foo.pdb"
> There was an error reading /home/epo/coot/foo.pdb.
> ERROR 42 READ: Duplicate sequence number and insertion code.
>  LINE #1571
>  ATOM   1666  N  BGLN B  93  24.448  28.340 -33.325  0.50 
> 9.34   N 
> 
> No Spacegroup found for this PDB file
> There was a coordinates read error
> 
> 
> One way to deal with it is to take the second conformer and manually add
> a sequence modifier (make it 93A), and that pdb file loads just fine.
> 
> This is observed with Coot-0.8.8-pre, rev.6506.
> 
> This is only a minor nuisance, of course, so I completely understand if
> no fix is made to load such strange models.
> 
> Cheers,
> 
> Ed.
> 
> ---
> Coot verendus est
> 
>