Chimera-dev October 2003

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chimera-dev@cgl.ucsf.edu

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12 discussions

database access
by Lars Kunert 10 Oct '03

10 Oct '03

Hi referring to my previous mail... what I am really doing is to write some kind of database interface. I see there basically three approaches - the first two are basically short-time workarounds ( I have decided to use the first one) there third would be the "real stuff" first) My plugin accesses the db and creates a temporary file - then it tells chimera to load it. Advantage chimera can use it native (and probably fast) reading routines... second) The plugin fetches the data form the db and builds up the molecule in chimera by use of the python-interface... third() I tell chimera to access the database X, use password Y, and run select / or call a stored procedure. the stored-procedure or (for older mysql a linked extension function) could build up an input-format chimera understands from the actual data. the select-version would be a bit ugly cause we would need several of them or place some file-blobs in the bd. I hope your are interested to do some thing about approach three... Sincerely Lars

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again Chimera and Dock
by Roberto Sanavio 03 Oct '03

03 Oct '03

Greetings to all, I'm a novice user of Chimera, and I downloaded it recently with the intention to use it also for calculating molecular surfaces as input for UCSF DOCK.From the documentation I haven't understood if the latest version of Chimera is able to do that. on Thu, 19 Dec 2002 Eric Pettersen wrote, answering to Eckhart Guthöhrlein , same date: "The current version of Chimera (12/02; build 1602) doesn't have the capability to prepare an ms file suitable for DOCK, though we anticipate that capability being in the next release (~ 3/03). " If, as I suspect, it's still not possible this use of Chimera, could you tell me if and when it will be?Do you perhaps know of alternatives still functioning on WindowsXP systems ( I'm a novice even about SGI ) or the better choice for me is still to study how to run old DMS on Irix? Thank you for your patience, Roberto Sanavio Politecnico di Milano tel. +39-031-513453 cell. +39347-5894996 e-mail: rsdag(a)libero.it

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