- Chimera-users - RBVI Mailing Lists

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

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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

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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

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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 -------

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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 -------

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Selection question in --nogui mode
by Miguel Ortiz Lombardia 26 May '05

26 May '05

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello. I'm trying to execute this: $chimera --nogui cmd:findselhbonds where the file findselhbonds contains: open 01.pdb select :59-62 hbonds selRestrict any saveFile tmp.bonds In the graphic mode those instructions work as expected, however in the - --nogui mode I get this error: Opening 01.pdb... warning: Ignored bad PDB record found on line 1 warning: Ignored bad PDB record found on line 2 Computed secondary structure assignments (see reply log) Model 0 (01.pdb) appears to be a protein with no secondary structure assignments. Computing assignments for it using the ksdssp algorithm (Kabsch and Sander Define Secondary Structure of Proteins) with an energy cutoff of - -0.5, minimum helix length of 5, and minimum strand length of 4. If these parameters don't produce good results for this structure, you can rerun the algorithm with different settings using the 'compute SS' button in the model panel (under 'infrequent' actions) or via the 'ksdssp' command in the Midas emulator. The model panel will also allow you to save new default parameters. 1 model opened Opened 01.pdb containing 1 model, 632 atoms, and 62 residues Error while processing cmd:forchimera: NameError: global name 'selMode' is not defined (see reply log for Python traceback info) Traceback (most recent call last): File "/usr/local/linux_prg/Chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 287, in init prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1043, in open File "CHIMERA/share/Midas/ChimeraExtension.py", line 17, in func File "CHIMERA/share/Midas/midas_text.py", line 88, in processCommandFile File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand File "CHIMERA/share/Midas/midas_text.py", line 1039, in doSelect File "CHIMERA/share/Midas/__init__.py", line 620, in chimeraSelect File "CHIMERA/share/chimera/tkgui.py", line 1604, in selectionOperation NameError: global name 'selMode' is not defined Any clues? Thank you very much! Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: miguel.ortiz(a)cnio.es - ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées >>> And the boring bits follow... -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.6 (GNU/Linux) iD8DBQFCleiGF6oOrDvhbQIRAi6cAJ415IJkwKrdjmhOofNbff34aEM3OQCeMdHj GNtxhKnI0DVyUDenbeAHOmw= =VDTj -----END PGP SIGNATURE----- **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Dipole
by Miguel Ortiz Lombardia 18 May '05

18 May '05

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all, Maybe a silly question, but I couldn't find anything in the docs. Given one structure pdb and an electrostatic potential calculated by delphi, can Chimera display the resulting dipole as a vector? Thank you very much! Cheers, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: miguel.ortiz(a)cnio.es - ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées >>> And the boring bits follow... -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.6 (GNU/Linux) iD8DBQFCi3u+F6oOrDvhbQIRAsvpAJ40rweZtnhVlp3HPYt8sVDODfzEjgCfdAyq efdpkP4wOqyWcrCTT23aJCM= =rxYo -----END PGP SIGNATURE----- **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Re: [Chimera-users] New 64-bit Linux version of Chimera
by Thomas Goddard 17 May '05

17 May '05

The 64-bit Linux Chimera 1.2123 installer was broken. A packaged file did not have execute permission. The fixed version is on the download page now with the same version number and date. If you got the broken version (by downloading in the past 8 hours), please try again. Sorry for the gaff. Tom

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Draw user specified object
by Reza Khayat 17 May '05

17 May '05

Hi, I was wondering if there is a way to draw a user specified object. For example, draw a cylinder (bond) from vertex x to vertex y. Thank you. Reza rkhayat(a)scripps.edu

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New 64-bit Linux version of Chimera
by Thomas Goddard 17 May '05

17 May '05

A new 64-bit Linux Chimera snapshot (version 1.2123) is available on the Chimera download page. http://www.cgl.ucsf.edu/chimera/download.html Unless you are viewing large data sets (> 1 Gb), we suggest you use 32-bit versions of Chimera on 64-bit Linux systems. 32-bit versions will likely run faster and use less memory. The 32-bit versions are more likely to be compatible with your Linux distribution. We are not yet making regular distributions for 64-bit linux so our 32-bit version will usually be newer. Tom

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