Print

Print


Yes, that would make a difference. :-)  Glad you got it worked out, and
thank you very much for sharing your solution here!


On Mon, Nov 5, 2018 at 6:26 PM Kit Sang Chu <[log in to unmask]> wrote:

> Hi Oliver and Lachele,
>
> Thanks for your reply. My "pentamer" is a heteromer which is consisted of
> two identical heterodimers and one monomer. They are not bonded covalently
> but through van der Waal's interaction. I managed to solve it by appending
> TER between each monomer. Now Glycam server can recognize them perfectly.
>
> Regards,
> Simon Kit Sang Chu
> Ph.D. student
> Biophysics Graduate Group
> University of California Davis
>
>
> On Mon, Nov 5, 2018 at 5:16 AM Oliver Grant <[log in to unmask]>
> wrote:
>
>> If I interpreted correct, perhaps protomer is the word to use instead of
>> peptide. In a PDB file sometimes each protomer of an oligomer will have
>> MODEL and END cards between each protomer. Try removing them. You can also
>> load the PDB file into something like USCF Chimera and rename the chains
>> and/or renumber the residues to be contiguous.
>>
>> If you can't get it to work, write us again. If you can provide the PDB
>> ID for your system that would be useful.
>>
>> Best,
>> Oliver
>>
>>
>> On Mon, Nov 5, 2018 at 1:52 PM Lachele Foley <[log in to unmask]> wrote:
>>
>>> We need some clarification.  Is the pentamer you speak of a peptide made
>>> of five amino acids?  If not that, then please specify.
>>>
>>> If you want to attach a glycan to a single, zwitterionic, amino acid,
>>> GLYCAM has, available for this purpose, variants of serine and threonine
>>> (residue names ZOLS and ZOLT).  If you want to model any other amino acids,
>>> or if you don't want the zwitterionic form, you will need to generate a
>>> residue with partial atomic charges.
>>>
>>> Our server will only detect that two cysteine residues are capable of
>>> forming a disulfide bond if their sulfur atoms are proximal.  For this to
>>> happen, your peptide will need to be uploaded in a conformation where that
>>> is the case.
>>>
>>> If none of what I just said answers your questions, then I didn't
>>> understand your situation.
>>>
>>>
>>> On Sun, Nov 4, 2018 at 1:26 AM Kit Sang Chu <[log in to unmask]> wrote:
>>>
>>>> Dear users of Glycam,
>>>>
>>>> I am a new user to Glycam and I am trying to build glycoprotein by
>>>> submitting a pentamer on Glycam server. However, Glycam only recognizes one
>>>> peptide with two terminals. Is there any specification on how Glycam server
>>>> recognizes monomer units?
>>>>
>>>> I also need disulfide bonds built. Submitting a pentamer directly
>>>> will therefore make things much more convenient.
>>>>
>>>> Regards,
>>>> Simon Kit Sang Chu
>>>> Ph.D. student
>>>> Biophysics Graduate Group
>>>> University of California Davis
>>>>
>>>
>>>
>>> --
>>> :-) Lachele
>>> Lachele Foley
>>> CCRC/UGA
>>> Athens, GA USA
>>>
>>

-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA