Re: [PyMOL] problem with amber trajectory]

Dmitry, is your system a single molecule or is it composed of multiple molecules (e.g. dimer)? Amber should not 'cut' your molecule into pieces, imaging can only separate molecules in a dimer, trimer or such. Also, was your system solvated? Did you strip water before visualizing in PyMOL? The

[Re: [PyMOL] combine distance objects]

ct hierarchy/grouping into PyMol may not be a trivial task... Cheers, -Viktor -- = Viktor Hornak Center for Structural Biology SUNY at Stony Brook =

[PyMOL] translating map/mesh

"alter_state" (alter_state 1,(mesh1),x=x+1.0, etc.) and undocumented "translate" (translate [1,1,1],mesh1) only work for atoms/molecules and not for arbitrary objects. Thanks for help, -Viktor -- Viktor Hornak SUNY at Stony Brook

Re: [PyMOL] PyMOL compatibility w/ NVidia card on rh9 system

the last line of the error, I suspect the problem has something to do with incompatibility between my rh9 installation and python interpreter as utilized by PyMOL? But I don't know enough to fix it Has anyone else seen (and fixed?) this problem?? -- Viktor Hornak SUNY at Stony Brook

[PyMOL] OT: firegl and stereo

org/gpc/opc.data/vp7/summary.html). However, the trick with these cards is to allow ATI's binary driver compatibility to dictate your choice of Linux distribution and version. This is fine for new dedicated 3D workstations (read SGI replacements), but not so good for existing linux setups.

Re: [PyMOL] ragged ends on rendered stick pictures

nes which have a fixed > rendered radius. the fix for this is to "hide lines, (selection)" > where selection is the atoms/bonds you want represented as thin sticks. > > zac > > > Viktor Hornak wrote: > > I've noticed another minor problem with internal ray

RE: [PyMOL] ragged ends on rendered stick pictures

not the 0.82 > windows release is affected) >By the way, I am well into the wrap-up process for a new release, > and am just trying to incorporate various bits of feedback from past > couple months. It will be out in a few weeks... -- ========

[PyMOL] amber support in CVS PyMOL

raj test.trj ..and here is where I got stuck, the message is: CmdLoadTraj-Error: must load object topology before loading trajectory! Was someone successful to get this working? Thanks very much, -Viktor -- === Viktor Hornak SUNY at Stony Brook Stony Brook, NY 11794-5115 E-mail: viktor.hor...@sunysb.edu ===

[PyMOL] amber support in CVS PyMOL

raj test.trj ..and here is where I got stuck, the message is: CmdLoadTraj-Error: must load object topology before loading trajectory! Was someone successful to get this working? Thanks very much, -Viktor -- === Viktor Hornak SUNY at Stony Brook Stony Brook, NY 11794-5115 E-mail: viktor.hor...@sunysb.edu ===

Re: [PyMOL] Stereographics CrystalEyes problem

PC (under W2K) with a Oxygen GVX card I had to use a "ENT" emitter from Stereographics. As far as I recall the regular emitters used on the SGI's, type "ESGI", did not work. Hope it helps. Cheers Carsten -Original Message- From: Viktor Hornak [mai

[PyMOL] Stereographics CrystalEyes problem

lp appreciated... Thanks, -Viktor -- ======= Viktor Hornak CSB computational facility SUNY at Stony Brook E-mail: viktor.hor...@sunysb.edu ===