Michael_E._Murphy@MTSG.UBC.CA (08/16/90)
I am intrested in molecular graphics software that is good at displaying electron density contours. We have been using FRODO on our 3000 series and I would like a 4D version. Is there anything better available? Has anyone experimented with something more realistic than wire cages? Michael Murphy usermbcm@mtsg.ubc.ca or @ubcmtsg.bitnet
doelz@urz.unibas.ch (08/16/90)
In article <2383953@mtsg.ubc.ca>, Michael_E._Murphy@MTSG.UBC.CA writes: > > I am intrested in molecular graphics software that is good at > displaying electron density contours. We have been using FRODO on > our 3000 series and I would like a 4D version. Is there anything > better available? Has anyone experimented with something more > realistic than wire cages? > We have been writing a prototype of program which does on-line contouring of density maps on a SGI 4D/120 resulting in shaded surfaces. Manipulation like scaling, rotation, translation and recontouring are done with dials. Split pair stereo is provided (and, StereoView will be running soon in our lab). The surfaces can be lighted, transparent, etc. A conversion utility for reformatting binary CCP4 VAX data is provided. The performance is great, the code is spagetti. Therefore, we are about redesigning it and will write it in C++. The problem of the program is that we do not reinvent the wheel, thus, need to have a package with a sufficiently open interface. There are some choices, and we did not conclude on a final package yet. - Reinhard
lnds@obed.uucp (Mark Israel) (08/17/90)
In article <2383953@mtsg.ubc.ca>, Michael_E._Murphy@MTSG.UBC.CA writes: > I am intrested in molecular graphics software that is good at > displaying electron density contours. We have been using FRODO on > our 3000 series and I would like a 4D version. Is there anything > better available? What we're currently using: 1) TOM/FRODO Contact: Christian Cambillau Address: Laboratoire de Cristallographie Faculte' de Me'decine Nord Boulevard Pierre Dramard 13326 Marseille cedex 15 France Phone: 33-91.65.79.47 Fax: 33-91.65.75.95 Licence fee: 2000 French francs TOM/FRODO is shipped with source code. (The source code is a mess, though). There is a "fixed up" version of this program with mods by Gary Griffin of SGI and by me. For details, send a message to "frodo-request@sgi.com". Coming "real soon now": 2) TURBO-FRODO Contact: Christian Cambillau Address, phone: as above Licence fee: U.S. $1000 to $2000 (depending on machine model) for academic users. 10 times as much for commercial users. Source code is not available. The beta-test version we have has many regressions from our fixed version of TOM/FRODO (e.g. there's no way to translate the model on the screen). These MAY be fixed in the next release. 3) CHAIN Contact: John Spurlino Address: Baylor College of Medicine Texas Medical Centre One Baylor Plaza Houston, Texas 77030 U.S.A. Phone: (713) 798-6563 E-mail: jcs@DINO.QCI.BIOCH.BCM.TMC.EDU Licence fee: not yet known. We got a free licence for one year. CHAIN is the best map-fitting program we've yet seen. The general policy will be not to release source. Currently there's nothing to skeletonize maps. 4) O (Yes, that's right, it's called "O".) Contact: Alwyn Jones Address: Dept. of Molecular Biology Biomedical Center, Uppsala University Box 590 S-751 24 Uppsala Sweden Phone: 018-174566 E-mail: ALWYN@BMC.UU.SE Licence fee: Probably around $250. For academic users only. The contract threatens a lawsuit if a commercial user gets ahold of it. We haven't even seen the test version of this yet, but we expect it in the next few weeks. Source will not be released. Mark Israel Bitnet: USERISRA@UALTAMTS Usenet: Mark_Israel@uqv-mts.alberta Internet: USERISRA@MTS.UCS.UALBERTA.CA