Multi-fragment fit in map
Good morning, I am EM user and I was wondering wether is possible in Chimera to fit multiple pdb in the same volume (e.g. Fitting two monomers into a dimer map without overlaps and clashes). I am using Situs and the collage command, but I was wondering if there was an easy way of doing it in Chimera. Thank you very much, Paolo Paolo Swuec, Ph.D. Student Architecture and Dynamics of Macromolecular Machines London Research Institute Clare Hall Laboratories Cancer Research UK South Mimms Herts EN6 3LD, UK E-mail: paolo.swuec@cancer.org.uk<mailto:alessandro.costa@cancer.org.uk> NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.
Good morning Paolo, Yes, there is "sequential fitting" using the "fitmap" command. See here for explanations including command options and link to a short video: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence> There is also symmetric fitting of multiple copies of the same structure: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#symmetric> I'd probably try the above first, but yet another related feature is MultiFit, which uses a web service (in menu under Tools… Volume Data): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multifit/multifit.html> 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 Nov 16, 2013, at 3:47 AM, Paolo Swuec <Paolo.Swuec@cancer.org.uk> wrote:
Good morning, I am EM user and I was wondering wether is possible in Chimera to fit multiple pdb in the same volume (e.g. Fitting two monomers into a dimer map without overlaps and clashes). I am using Situs and the collage command, but I was wondering if there was an easy way of doing it in Chimera. Thank you very much, Paolo
participants (2)
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Elaine Meng -
Paolo Swuec