[Chimera-users] my question

David Bhella David.Bhella at glasgow.ac.uk
Mon Jan 25 12:37:15 PST 2016


I think I answered a similar enquiry on this mailing list a few years back. PRRSV is not thought to be an icosahedral virus, so far as I know so it will not be possible to assemble a virion model from pdb files.
Terje Dokland published a paper on this by tomography.
Reviewed here

http://www.ncbi.nlm.nih.gov/m/pubmed/20692304

Sent from my iPhone

> On 25 Jan 2016, at 19:42, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Dear Yanli Li,
> Chimera does not predict structures.   If the solved parts already have symmetry matrix information in their files, Chimera can use these matrices to assemble their multimers (see Multiscale Models tool or “sym” command).  You could also interactively assemble parts in Chimera with the mouse based on your own knowledge such as information from the literature, known homologous structures and related viruses, or data such as an EM map into which you could semi-manually fit the crystal structures.
> 
> As far as I understand it, “nsp” means nonstructural protein, so you would mainly be interested in the nucleocapsid structure.  I searched the RCSB PDB and found this structure 1p65
> <http://www.rcsb.org/pdb/explore/explore.do?structureId=1P65>
> 
> … but it is only a fragment, and it does not contain the symmetry information that would be needed to build up a whole particle.  So you would probably need to try to figure out if there are other similar viruses or known homologous proteins with more complete structure information, and think about whether they are similar enough to help you model PRRSV. 
> 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 Jan 25, 2016, at 9:07 AM, Yanli Li <yanli.li at e-campus.uab.cat> wrote:
>> 
>> Dear sirs/madams,
>> 
>> I am a PhD student in Universitat Autònoma de Barcelona. I am working on the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV). I have got differences of cytokine profiles and phenotype regulation of antigen presenting cells by different isolates through the lab work. Now I intend to predict the structure of the whole or some parts of the viral particle with UCSF CHIMERA. However, there are only three relevant structures(nucleocapsid, nsp1, nsp4) that have been published. Is it possible to realize it? If yes, can you tell me the method in brief? Thanks a lot!
>> 
>> Waiting for your reply.
>> 
>> Best wishes,
>> 
>> Yanli LI
> 
> 
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