Re: [PyMOL] trying to build cyclic peptides with PyMOL
Hi Moshe, No it isn't. PyMOL is a molecular viewer/graphics engine, not a modeling package. However, it's not too hard to do using your favourite MD package. With the definition of a bond and some energy minimization you'd get close. If it's for displaying purposes only, that might even be enough. Cheers, Tsjerk On Fri, Feb 15, 2008 at 1:17 AM, wrote: > > Hello. > > I am new to PyMOL. > Very easily I succeeded to build a linear peptide, given its sequence. > I want to build a cyclic peptide for the same sequence, connecting the > C-terminus with the N-terminus. I know that the bond that is created > that way is too long - it should be, also, some > (automatic/algorithmic) way to rearrange the cyclic structure in order > to have an acceptable bond length. > Is this possible to do with PyMOL? > > Thanks for your help. > -- Moshe Goldstein > > > > > This message was sent using IMP, the Internet Messaging Program. > > > - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
Re: [PyMOL] trying to build cyclic peptides with PyMOL
For an analytical solution to the cyclic peptide problem, see N Go and HA Scheraga, Macromolecules 6, 273 (1973). For an application to modeling of the cyclic peptide gramicidin S, see M Dygert, N Go and HA Scheraga Macromolecules 8, 750-761, 1975. Kathleen P. Pratt, Ph.D. Assistant Member Puget Sound Blood Center 921 Terry Avenue Benaroya Research Institute, Rm. 3016 Seattle, WA 98104 ph 206-398-5921 FAX 206-587-6056 email kathle...@psbc.org -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of goldm...@fh.huji.ac.il Sent: Thursday, February 14, 2008 4:18 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] trying to build cyclic peptides with PyMOL Hello. I am new to PyMOL. Very easily I succeeded to build a linear peptide, given its sequence. I want to build a cyclic peptide for the same sequence, connecting the C-terminus with the N-terminus. I know that the bond that is created that way is too long - it should be, also, some (automatic/algorithmic) way to rearrange the cyclic structure in order to have an acceptable bond length. Is this possible to do with PyMOL? Thanks for your help. -- Moshe Goldstein This message was sent using IMP, the Internet Messaging Program. - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users * This e-mail and any attachments may contain confidential and privileged information. It has been scanned for viruses. If you are not the intended recipient, please notify the sender immediately by return e- mail, delete this e-mail and destroy any copies. Any dissemination, use, review, disclosure, or distribution of this information by a person other than the intended recipient is unauthorized and may be illegal. * **
Re: [PyMOL] trying to build cyclic peptides with PyMOL
Thank you for those references - I will look on them. Do you think they will help in actually building a cyclic peptide with PyMOL? Thanks again. -- Moshe Goldstein Quoting Kathleen Pratt : For an analytical solution to the cyclic peptide problem, see N Go and HA Scheraga, Macromolecules 6, 273 (1973). For an application to modeling of the cyclic peptide gramicidin S, see M Dygert, N Go and HA Scheraga Macromolecules 8, 750-761, 1975. Kathleen P. Pratt, Ph.D. Assistant Member Puget Sound Blood Center 921 Terry Avenue Benaroya Research Institute, Rm. 3016 Seattle, WA 98104 ph 206-398-5921 FAX 206-587-6056 email kathle...@psbc.org -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of goldm...@fh.huji.ac.il Sent: Thursday, February 14, 2008 4:18 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] trying to build cyclic peptides with PyMOL Hello. I am new to PyMOL. Very easily I succeeded to build a linear peptide, given its sequence. I want to build a cyclic peptide for the same sequence, connecting the C-terminus with the N-terminus. I know that the bond that is created that way is too long - it should be, also, some (automatic/algorithmic) way to rearrange the cyclic structure in order to have an acceptable bond length. Is this possible to do with PyMOL? Thanks for your help. -- Moshe Goldstein This message was sent using IMP, the Internet Messaging Program. - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users * This e-mail and any attachments may contain confidential and privileged information. It has been scanned for viruses. If you are not the intended recipient, please notify the sender immediately by return e- mail, delete this e-mail and destroy any copies. Any dissemination, use, review, disclosure, or distribution of this information by a person other than the intended recipient is unauthorized and may be illegal. * ** This message was sent using IMP, the Internet Messaging Program.
Re: [PyMOL] trying to build cyclic peptides with PyMOL
I need to build a cyclic peptide as the initial conformation for further simulations, not only for displaying purposes. I will try what you say and I will see. Thank you. -- Moshe Goldstein Quoting Tsjerk Wassenaar : Hi Moshe, No it isn't. PyMOL is a molecular viewer/graphics engine, not a modeling package. However, it's not too hard to do using your favourite MD package. With the definition of a bond and some energy minimization you'd get close. If it's for displaying purposes only, that might even be enough. Cheers, Tsjerk On Fri, Feb 15, 2008 at 1:17 AM, wrote: Hello. I am new to PyMOL. Very easily I succeeded to build a linear peptide, given its sequence. I want to build a cyclic peptide for the same sequence, connecting the C-terminus with the N-terminus. I know that the bond that is created that way is too long - it should be, also, some (automatic/algorithmic) way to rearrange the cyclic structure in order to have an acceptable bond length. Is this possible to do with PyMOL? Thanks for your help. -- Moshe Goldstein This message was sent using IMP, the Internet Messaging Program. - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 This message was sent using IMP, the Internet Messaging Program.
