[phenixbb] Glycan Links/Restraints

Engin Özkan eozkan at stanford.edu
Mon Feb 28 23:44:46 PST 2011


Also, I just remembered that Phenix/monomer library may still not have 
BMA and MAN right. You may have to provide MAN and/or BMA cif files with 
the correct stereochemistries. Monomer library does not necessarily 
follow the standards of the PDB chemical component library (but 
obviously, PDB enforces them).

Finally, you can always check the .geo file that phenix.refine produces, 
and you will find all the applied restraints. That should definitively 
tell you your problem.

Engin

On 2/28/11 10:36 PM, Engin Özkan wrote:
> Dear Damien,
>
> Let me make a guess: You have the BETA1-4 linkages in the wrong order. 
> If you look in the mon_lib_list.cif file, you can find the line where 
> it says:
>  BETA1-4  1 O4      2 C1        single       1.439    0.020
> which tells me that the residue to be defined (residue_selection_1) 
> ought to be the atom atom connecting with the O4 atom (the inner 
> glycan) and the second residue is the one with the C1 atom (the outer 
> glycan). So try switching residue_selection_1 and _2 for your BETA1-4 
> linkages. I know you are probably thinking BETA1-4 should go 1 to 4, 
> but that is not how it is defined in the monomer library. By the way, 
> your NAG-ASN linkages do look correct, and you have the correct 
> anomers for beta-mannose (BMA) and alpha-mannose (MAN), which is where 
> most people seem to get stuck.
>
> One stylistic question I have for you is, why are you naming your 
> protein and glycans with different chain IDs; aren't they actually 
> covalently linked? There apparently is no right way for numbering 
> glycan residues, and everybody seems to be do a different thing...
>
> Good luck,
> Engin
>
> On 2/28/11 6:39 PM, Damian Ekiert wrote:
>> Sorry to bring up an old topic again but I can't find any 
>> documentation of glycan refinement on the Phenix website and previous 
>> threads don't seem to answer my question.
>>
>> I am refining a structure with N-linked glycans.  I have inserted 
>> several "apply_cif_link" records to my .eff file to define the glycan 
>> topologies (see below) and fed in a cif file for BMA.  After fiddling 
>> for quite some time now, I have managed to get around all the error 
>> messages people have described previously to disappear.  Yet, 1) none 
>> of my linkages appear to be enforced and 2) even the restraints on 
>> the individual sugars appear to be unenforced (or at least, 
>> insufficiently so).  For example, some rings are rendered almost 
>> flat, or flipped into boat or otherwise distorted conformations, and 
>> glycosidic bonds stretch to>2 A.
>>
>> No obvious signs of trouble in the log file, running the latest 
>> version (1.7, also tried 1.6.4), but my glycans look terrible 
>> (despite some of the best density I have ever seen!  :-)  )
>>
>> Any suggestions would be appreciated!
>>
>> Thanks,
>>
>> Damian Ekiert
>>
>>
>>
>>  From my .eff file:
>>
>>      apply_cif_link {
>>        data_link = NAG-ASN
>>        residue_selection_1 = chain X and resname NAG and resid 401
>>        residue_selection_2 = chain A and resname ASN and resid 91
>>      }
>>      apply_cif_link {
>>        data_link = NAG-ASN
>>        residue_selection_1 = chain Y and resname NAG and resid 401
>>        residue_selection_2 = chain C and resname ASN and resid 91
>>      }
>>      apply_cif_link {
>>        data_link = NAG-ASN
>>        residue_selection_1 = chain Z and resname NAG and resid 401
>>        residue_selection_2 = chain E and resname ASN and resid 91
>>      }
>>      apply_cif_link {
>>        data_link = BETA1-4
>>        residue_selection_1 = chain X and resname NAG and resid 402
>>        residue_selection_2 = chain X and resname NAG and resid 401
>>      }
>>      apply_cif_link {
>>        data_link = BETA1-4
>>        residue_selection_1 = chain Y and resname NAG and resid 402
>>        residue_selection_2 = chain Y and resname NAG and resid 401
>>      }
>>      apply_cif_link {
>>        data_link = BETA1-4
>>        residue_selection_1 = chain Z and resname NAG and resid 402
>>        residue_selection_2 = chain Z and resname NAG and resid 401
>>      }
>>      apply_cif_link {
>>        data_link = BETA1-4
>>        residue_selection_1 = chain Y and resname BMA and resid 403
>>        residue_selection_2 = chain Y and resname NAG and resid 402
>>      }
>>      apply_cif_link {
>>        data_link = ALPHA1-3
>>        residue_selection_1 = chain Y and resname MAN and resid 404
>>        residue_selection_2 = chain Y and resname BMA and resid 403
>>      }
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>
>


-- 
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111




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