To whom it may concern, I am a chimera user and am currently doing a glycan research using Chimera 1.5.3. I wonder if chimera has a function to add glycans to a protein. Thank You. Sincerely, Pek Ieong
Dear Pek Leong, There is nothing specific for building glycans. However, if you already had separate structures of the glycan part and the protein, you could use Build Structure (under Tools... Structure Editing), the Join Models tab to attach them. This will simply attach the structures -- it will not predict reasonable conformations. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join> Some possible sources of the glycan part would be some other PDB structure (you could just delete the parts you don't want) or if it is in the PubChem compound database, fetching by CID # into Chimera (for example, command: open pubchem:4582185 ) <http://www.ncbi.nlm.nih.gov/pccompound?term=glycan> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 6, 2011, at 12:58 AM, Flora Ieong wrote:
To whom it may concern, I am a chimera user and am currently doing a glycan research using Chimera 1.5.3. I wonder if chimera has a function to add glycans to a protein. Thank You. Sincerely, Pek Ieong
Thank You. The information is very helpful ________________________________ 從︰ Elaine Meng <meng@cgl.ucsf.edu> 收件人︰ Flora Ieong <ice_pek@yahoo.com.hk> 副本(CC)︰ "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> 傳送日期︰ 2011年07月6日 (週三) 11:08 AM 主題︰ Re: [Chimera-users] Chimera function Dear Pek Leong, There is nothing specific for building glycans. However, if you already had separate structures of the glycan part and the protein, you could use Build Structure (under Tools... Structure Editing), the Join Models tab to attach them. This will simply attach the structures -- it will not predict reasonable conformations. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join> Some possible sources of the glycan part would be some other PDB structure (you could just delete the parts you don't want) or if it is in the PubChem compound database, fetching by CID # into Chimera (for example, command: open pubchem:4582185 ) <http://www.ncbi.nlm.nih.gov/pccompound?term=glycan> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 6, 2011, at 12:58 AM, Flora Ieong wrote:
To whom it may concern, I am a chimera user and am currently doing a glycan research using Chimera 1.5.3. I wonder if chimera has a function to add glycans to a protein. Thank You. Sincerely, Pek Ieong
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Elaine Meng -
Flora Ieong