Hi Elaine I am trying to use the sym command to generate BIOMT-described copies of a protein. As a test I have used 2oli, as in your contribution of 12 Jan 2009. Having loaded 2oli and entered the command sym #0 #0 I get the error message "No symmetric molecule copies". Any help gratefully received Anthony Lee
Hi Anthony, You must be referring to this message: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003446.html> The PDB ID in that message contains “1” number one not “l” letter ell. So if you use 2o1i which is a DNA, your command will work. It does not do anything with 2oli because that protein monomer is already the biological assembly, at least according to its page at RCSB: <https://www.rcsb.org/structure/2oli> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 9, 2018, at 5:03 AM, Lee A.G. <A.G.Lee@soton.ac.uk> wrote:
Hi Elaine I am trying to use the sym command to generate BIOMT-described copies of a protein. As a test I have used 2oli, as in your contribution of 12 Jan 2009. Having loaded 2oli and entered the command sym #0 #0 I get the error message "No symmetric molecule copies". Any help gratefully received Anthony Lee
Hi Elaine Very many thanks for clearing that up for me! I was hoping that there was something in Chimera like the symexp command in PyMol that takes a protein and then creates all its crystallographic neighbours (all symmetry related objects) within a given cut-off distance from the original molecule. I think that what I will have to do is to generate the symmetry-related molecules using PyMol, save them as PDB files, and then open them in Chimera for further handling. Many thanks once again Anthony ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: 09 July 2018 18:17 To: Lee A.G. Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Use of sym command Hi Anthony, You must be referring to this message: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003446.html> The PDB ID in that message contains “1” number one not “l” letter ell. So if you use 2o1i which is a DNA, your command will work. It does not do anything with 2oli because that protein monomer is already the biological assembly, at least according to its page at RCSB: <https://www.rcsb.org/structure/2oli> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 9, 2018, at 5:03 AM, Lee A.G. <A.G.Lee@soton.ac.uk> wrote:
Hi Elaine I am trying to use the sym command to generate BIOMT-described copies of a protein. As a test I have used 2oli, as in your contribution of 12 Jan 2009. Having loaded 2oli and entered the command sym #0 #0 I get the error message "No symmetric molecule copies". Any help gratefully received Anthony Lee
Hi Anthony, See the Unit Cell tool (in menu under Tools... Higher-Order Structure). You have a choice of which symmetry information to use and/or how many unit cells, etc. Of course, you have to choose a structure that has such symmetry information in the first place: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html> Unit Cell can use any/all of the crystallographic symmetry information, but it doesn’t use BIOMT (biological unit) information. One can apply BIOMT symmetry with the “sym” command or the Multiscale Models tool (also under Tools… Higher-Order Structure). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 10, 2018, at 5:08 AM, Lee A.G. <A.G.Lee@soton.ac.uk> wrote:
Hi Elaine Very many thanks for clearing that up for me! I was hoping that there was something in Chimera like the symexp command in PyMol that takes a protein and then creates all its crystallographic neighbours (all symmetry related objects) within a given cut-off distance from the original molecule. I think that what I will have to do is to generate the symmetry-related molecules using PyMol, save them as PDB files, and then open them in Chimera for further handling. Many thanks once again Anthony
Hi Anthony, You can make copies of a molecule using crystal symmetry in Chimera with the crystalcontacts command: open 2o1i crystalcontacts #0 5 copies true schematic false This makes copies within 5 Angstroms of 2o1i. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/crystalcontacts.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/crystalcontacts.html> Tom
On Jul 10, 2018, at 5:08 AM, Lee A.G. <A.G.Lee@soton.ac.uk> wrote:
Hi Elaine Very many thanks for clearing that up for me! I was hoping that there was something in Chimera like the symexp command in PyMol that takes a protein and then creates all its crystallographic neighbours (all symmetry related objects) within a given cut-off distance from the original molecule. I think that what I will have to do is to generate the symmetry-related molecules using PyMol, save them as PDB files, and then open them in Chimera for further handling. Many thanks once again Anthony
________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: 09 July 2018 18:17 To: Lee A.G. Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Use of sym command
Hi Anthony, You must be referring to this message: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003446.html>
The PDB ID in that message contains “1” number one not “l” letter ell. So if you use 2o1i which is a DNA, your command will work. It does not do anything with 2oli because that protein monomer is already the biological assembly, at least according to its page at RCSB: <https://www.rcsb.org/structure/2oli>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 9, 2018, at 5:03 AM, Lee A.G. <A.G.Lee@soton.ac.uk> wrote:
Hi Elaine I am trying to use the sym command to generate BIOMT-described copies of a protein. As a test I have used 2oli, as in your contribution of 12 Jan 2009. Having loaded 2oli and entered the command sym #0 #0 I get the error message "No symmetric molecule copies". Any help gratefully received Anthony Lee
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participants (3)
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Elaine Meng -
Lee A.G. -
Tom Goddard