Visualization Martini coarse grained model in Chimera
Dear All It is possible to visualize martini coarse grained bead of proteins and lipid in Chimera? if yes please guide me for same. Thanks & regards Rahman ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' *M*d* H*omaidur* R**ahman *( Research Scholar ) Lab No. 510, Computational Biophysics Lab. Department of Biotechnology Indian Institute of Technology-Madras Chennai-600 036, India *Mobile No = +91- 7845991785* '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
Dear Rahman, Although we have not tried it ourselves, it must be possible because some other user has done it using version 1.10.2 or later, as mentioned in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-May/012295.html> That user had the Martini trajectory in the Gromacs format, so I guess you would need to use that format too. You would start the “MD Movie” tool (Tools… MD/Ensemble Analysis… MD Movie) and specify the input Gromacs files (.tpr file and .trr or .xtc file). There are lots of features in MD Movie, see the manual: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h... 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 8, 2017, at 9:04 PM, MOHD HOMAIDUR RAHMAN <rahmanhpu@gmail.com> wrote:
Dear All
It is possible to visualize martini coarse grained bead of proteins and lipid in Chimera? if yes please guide me for same.
Thanks & regards Rahman
Dear Elaine Thank you very much this is working for me. I am always facing problem, when I am using chimera for bigger system like virus or large no of proteins in my systems. Is there any special taking care needed during installation? What we will do to improve speed, for example I am able to load gromacs TPR and XTC file but unable to rotate or zoom in/out of my system. Thanks & regards Rahman
Dear Rahman, Unfortunately as far as I know you cannot do much, other than to use the best system (newer computer with more memory) that is available to you. We realize that Chimera is slow on very large structures and datasets, and we are developing the new program ChimeraX for high-performance rendering of large structures. However, ChimeraX is still in early development and does not have a tool like MD Movie or support for reading the gromacs files. Regards, 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 12, 2017, at 10:57 PM, MOHD HOMAIDUR RAHMAN <rahmanhpu@gmail.com> wrote:
Dear Elaine
Thank you very much this is working for me. I am always facing problem, when I am using chimera for bigger system like virus or large no of proteins in my systems. Is there any special taking care needed during installation? What we will do to improve speed, for example I am able to load gromacs TPR and XTC file but unable to rotate or zoom in/out of my system. Thanks & regards Rahman
Dear Elaine Thanks again for prompt reply. Here you talking about RAM or system home memory where chimera install. Regards Rahman ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' *M*d* H*omaidur* R**ahman *( Research Scholar ) Lab No. 510, Computational Biophysics Lab. Department of Biotechnology Indian Institute of Technology-Madras Chennai-600 036, India *Mobile No = +91- 7845991785* ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' On Fri, Jan 13, 2017 at 10:31 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Rahman, Unfortunately as far as I know you cannot do much, other than to use the best system (newer computer with more memory) that is available to you. We realize that Chimera is slow on very large structures and datasets, and we are developing the new program ChimeraX for high-performance rendering of large structures. However, ChimeraX is still in early development and does not have a tool like MD Movie or support for reading the gromacs files. Regards, 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 12, 2017, at 10:57 PM, MOHD HOMAIDUR RAHMAN <rahmanhpu@gmail.com> wrote:
Dear Elaine
Thank you very much this is working for me. I am always facing problem, when I am using chimera for bigger system like virus or large no of proteins in my systems. Is there any special taking care needed during installation? What we will do to improve speed, for example I am able to load gromacs TPR and XTC file but unable to rotate or zoom in/out of my system. Thanks & regards Rahman
Dear Rahman, RAM, I think, but my coworkers know much more about hardware than I do. Maybe this previous post will be helpful: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-September/010316.html> Regards, Elaine On Jan 13, 2017, at 9:38 PM, MOHD HOMAIDUR RAHMAN <rahmanhpu@gmail.com> wrote:
Dear Elaine Thanks again for prompt reply. Here you talking about RAM or system home memory where chimera install. Regards Rahman
On Fri, Jan 13, 2017 at 10:31 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Rahman, Unfortunately as far as I know you cannot do much, other than to use the best system (newer computer with more memory) that is available to you. We realize that Chimera is slow on very large structures and datasets, and we are developing the new program ChimeraX for high-performance rendering of large structures. However, ChimeraX is still in early development and does not have a tool like MD Movie or support for reading the gromacs files.
Yes: RAM, not disk space. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 14, 2017, at 8:39 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Rahman, RAM, I think, but my coworkers know much more about hardware than I do. Maybe this previous post will be helpful:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-September/010316.html>
Regards, Elaine
On Jan 13, 2017, at 9:38 PM, MOHD HOMAIDUR RAHMAN <rahmanhpu@gmail.com> wrote:
Dear Elaine Thanks again for prompt reply. Here you talking about RAM or system home memory where chimera install. Regards Rahman
On Fri, Jan 13, 2017 at 10:31 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Rahman, Unfortunately as far as I know you cannot do much, other than to use the best system (newer computer with more memory) that is available to you. We realize that Chimera is slow on very large structures and datasets, and we are developing the new program ChimeraX for high-performance rendering of large structures. However, ChimeraX is still in early development and does not have a tool like MD Movie or support for reading the gromacs files.
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participants (3)
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Elaine Meng -
Eric Pettersen -
MOHD HOMAIDUR RAHMAN