June 2005 - Chimera-users - RBVI Mailing Lists

How to append functional groups to a residue
by C. Parry 01 Jul '05

01 Jul '05

Hi Chimera Peoples - My question is how does one append a functional group (say, nitro, bromine, ..., or metal) to a residue (say, tyrosine, ..., adenine). This would involve replacing some atom or group. I am aware of 'swapa,' 'swapna' commands but these are straight forward one-for-one changes of whole residues. Thanks. C. Parry __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

2 1

Exporting 3D File Formats
by peter allen 30 Jun '05

30 Jun '05

Hello, Does your software have any way of exporting 3d file formats. DXF OBJ 3DS IGES STL DWG etc Many Thanks Peter Allen

2 1

Gallery PDB source
by David Piper 24 Jun '05

24 Jun '05

Chimera Folks, I was looking at the gallery images and noticed that one is of the FlAsH molecule. Are the PDB coordinate available somewhere for this molecule? Or ReAsH? Thanks, David

2 1

Electron density
by C. Parry 22 Jun '05

22 Jun '05

Could anyone help with loading and displaying CNS or XPLOR electron density maps in Chimera. I have tried many times and also the dialog boxes in the user guide do not exactly correspond to the version (12/2004) of Chimera I have. Thanks. ____________________________________________________ Yahoo! Sports Rekindle the Rivalries. Sign up for Fantasy Football http://football.fantasysports.yahoo.com

3 2

mutation tool?
by ROBERT LAVIERI 17 Jun '05

17 Jun '05

I am exploring/using the program and I was wondering if there was any sort of point mutation tool? Such that one could graphically see say a mutation like ser23trp? Thanks, Robert R Lavieri

2 1

how to open bug-report dialog in v1.2105
by Sabuj Pattanayek 13 Jun '05

13 Jun '05

Hi, In v1.2105 (irix) the report a bug command under the help menu is not available (as stated in the current development documentation I assume for v1.2129). How do I open the bug report submission dialog from the command line or from the menus even if a crash or error has not occurred? Thanks, Sabuj Pattanayek

2 1

Stereo monitors
by Thomas Goddard 06 Jun '05

06 Jun '05

Steve Ludtke reports what his lab is using for hardware stereo. Tom ------- Start of forwarded message ------- Date: Mon, 6 Jun 2005 12:59:39 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: Chimera Suggestion We have the Sharp 15" one. As I said, it works ok as long as you stay in the sweet spot, but gives me a nasty headache (which the glasses do not). We haven't tried any of the high-refresh LCD's yet. We still use CRT's for that at the moment. We're about to try a homebrew polarized glasses solution. We do actually have a (800x600) high refresh projector for use with the shutter glasses which works well. - ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Asst. Professor & Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-9020 | Dept of Biochemistry and Mol. Biol. F: (713)798-1625 | instant messenger: sludtke42 | Those who Do, Are http://ncmi.bcm.tmc.edu/~stevel | The converse also applies On Mon, 6 Jun 2005, Thomas Goddard wrote: > Hi Steve, > > Our stereo monitor that requires no glasses was a 20" flat panel > type display from Opticality (formerly X3D). I just found out we have > returned it because it worked so poorly. I'd be curious what > make/model you have. Also have you tried any normal flat panels with > fast refresh rates and LCD glasses? > > Tom > ------- End of forwarded message -------

1 0

Red / blue stereo
by Thomas Goddard 06 Jun '05

06 Jun '05

Steve Ludtke would like red / blue stereo. Tom ------- Start of forwarded message ------- Date: Sat, 4 Jun 2005 02:13:29 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Chimera Suggestion We've had a minor resurgance of stereo work in the lab recently. We have a couple of SGI's still with the standard shutter-glasses, and a single PC with a CRT and an active stereo capable projector. We tried the Sharp autostereographic monitor, but it works only so-so, and gives me a headache almost instantly. It would be really useful to have simple stereo set up for occasional use on all of the desktop machines in the lab (which have normal LCD panels now). Anyway, I was just wondering if you guys thought about implementing analglyph (red/blue glasses) stereo ? I've done this manually for snapshots using the 'left eye' and 'right eye' mode in chimera to get the separation right, and it works surprisingly well as long as you don't mind sacrificing color. It would be very useful to have this available for interactive use. Any chance ? (it's also very useful for posters, since many people can't do the eye-crossing thing). Just a suggestion :^) - ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Asst. Professor & Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-9020 | Dept of Biochemistry and Mol. Biol. F: (713)798-1625 | instant messenger: sludtke42 | Those who Do, Are http://ncmi.bcm.tmc.edu/~stevel | The converse also applies ------- End of forwarded message -------

1 0

Chimera-users June 2005