July 2009 - Chimera-users - RBVI Mailing Lists

icosahedral cage
by Kristin Parent 17 Jul '09

17 Jul '09

does anyone know if there is a way to increase the line thickness of the icosahedron cage in the higher-order structures option? Can't seem to figure it out. Thanks in advance. Kristin Kristin Parent, Ph.D. University of California, San Diego Department of Chemistry and Biochemistry 9500 Gilman Drive, NSB 4104A, MC-0378 La Jolla, CA, 92093-0378 (858) 534-8038

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chimera crash in windows vista
by justin oppenheim 17 Jul '09

17 Jul '09

Hello: When I invoke chimera, it crashes with the message: "chimera failed abnormally; the exit code was 1. Use the --debug ...." Then when I execute the "chimera debug" from the list of all the installed progems, I get (in a prompt windows): Traceback (most recent call last): File "C:\Program Files\chimera\share\_main_.py, line 65, in (module) value=chimeraInit.init(sys.argv) File "C:\Program Files\chimera\share\chimeraInit.py", line 361 in init tkgui.initializeGUI(exitonquit,debug_opengl) TypeError:initializeGUI() takes exactly 1 argument (2 given) Return code: 1Press return or enter to to exit What can I do now. Please help! Thanks,JO

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color scale bar
by Yao Cong 17 Jul '09

17 Jul '09

Hello Chimera developer, I am rendering a PDB file colored according to B-factor value by "render by attribute" tool. How can I generate a color scale bar besides the structure labeling the color scale used? Many thanks, Yao Cong

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Re: [Chimera-users] missing chimera-users email
by Eric Pettersen 17 Jul '09

17 Jul '09

I see what happened to the mail now. Cao is not a subscriber to chimera-users so her mail was held up for moderator approval. I'll fix that now... --Eric On Jul 16, 2009, at 5:46 PM, Greg Couch wrote: > So it's not in the archive nor does Tom Goddard have it, so you'll > have to forward it to me :-). > > - Greg

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Re: [Chimera-users] Chimera-users Digest, Vol 75, Issue 17
by Burkhard Heil 15 Jul '09

15 Jul '09

Liebste, hab jetzt auch AB abgehört:-) und warte auf meine gesättigte oder essende Sarah:-) Knutschknutsch! Küsse Dein Burkhard On 14.07.2009, at 21:00, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. suggestion/transform molecule coordinates (Dougherty, Matthew T.) > 2. Re: suggestion/transform molecule coordinates (Thomas Goddard) > 3. Re: sequence viewer (Eric Pettersen) > 4. Re: sequence viewer (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Jul 2009 15:30:21 -0500 > From: "Dougherty, Matthew T." <matthewd(a)bcm.tmc.edu> > Subject: [Chimera-users] suggestion/transform molecule coordinates > To: <chimera-users(a)cgl.ucsf.edu> > Message-ID: > <B5CA7C88183F884CB316B04DCD343849013465D6(a)BCMEVS13.ad.bcm.edu> > Content-Type: text/plain; charset="iso-8859-1" > > relating to the apply, close & help buttons > > 1)"reset" button > The reset would remove prior transformations > > 2) "apply once" button. > The apply once would function the same as a reset and apply in > sequence. > > 3) display sum of current transformation (Euler & shift) > > > Matthew Dougherty > 713-433-3849 > National Center for Macromolecular Imaging > Baylor College of Medicine/Houston Texas USA > = > = > = > ====================================================================== > = > = > = > ====================================================================== > > >

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Re: [Chimera-users] [chimera-dev] Non-standard residues
by Elaine Meng 15 Jul '09

15 Jul '09

Hi Alex, The calculation requires parameters for all of the atoms present regardless of whether they are frozen during minimization or not. The frozen atoms still exert forces on the movable atoms. Unfortunately there is a hard limitation on which metal ions can be handled. Possible workarounds have been discussed on chimera-users, for example: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-July/004066.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003682.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 14, 2009, at 4:56 PM, Alex Gawronski wrote: > Hello, > > I used :/!isHet for the "spec" option for "minimize" and I'm still > getting "Unable to find GAFF type for #0:155.A@FE " for 101M. I > thought this would skip the heme, but I guess not. How can I avoid > this error? > > Thanks again! > > Alex >

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dragging a displayed object
by justin oppenheim 15 Jul '09

15 Jul '09

Hello: I am displaying two or more very similar objects, but they are shifted one with respect to another. How can I drag/move/align them on the display to correct for the relative shift? Many thanks, JO

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Some problem with volume coloring
by MAG 14 Jul '09

14 Jul '09

Good day for you, Would be so kind and help me. The problem is I want to color two parts of my volume. So, I have put markers inside of it, color two parts, but now I want to save this colored volume, such that after I would be able to duplicate it and use as a normal volume, but colored. Thank you in advance, Best, Alex

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sequence viewer
by Gatsogiannis, Christos 13 Jul '09

13 Jul '09

Hi all, i ve just installed the latest daily build version and i´ve noticed that the sequence viewer has a new "look". However, i have difficulties to get used to it... Some examples: -when i want to view the sequence of a pdb file containing seven chains, i get seven different pop-up windows (...) showing the sequences corresponding to the seven different chain ID´s.... -Moreover, it isn´t so "easy" anymore to select aminoacids directly in the sequence viewer (e.g. too many colors) and therefore now i´m selecting residues using only the command line.. My colleagues also prefer the older version.. is there a simple way to install the latest chimera version but keep the old version of the sequence viewer? Thanks! -Christos ------------------------------- Christos Gatsogiannis Insitute of Zoology, Dpt. II cryoEM Lab, AG Markl Joh. v. Müllerweg 6 Johannes Gutenberg University Mainz, Germany +49-6131-3923091 ------------------------------- ________________________________________ Von: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] im Auftrag von chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Gesendet: Mittwoch, 17. Dezember 2008 21:00 An: chimera-users(a)cgl.ucsf.edu Betreff: Chimera-users Digest, Vol 68, Issue 22 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: (Thermal ellipsoids) anisotropic temperature factor ellipsoids (Eric Pettersen) 2. Re: (Thermal ellipsoids) anisotropic temperature factor ellipsoids (Eric Pettersen) 3. possibilities to save parts of models (selection)? (Sebastian Kruggel) 4. Re: possibilities to save parts of models (selection)? (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 16 Dec 2008 14:59:34 -0800 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids To: Tom Goddard <goddard(a)cgl.ucsf.edu> Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> Message-ID: <9A34751B-6356-4AF4-A8C7-31757E5FFBF1(a)cgl.ucsf.edu> Content-Type: text/plain; charset="us-ascii" On Dec 12, 2008, at 10:40 AM, Tom Goddard wrote: > Hi David, > > Ok I see now, it's a matter of choosing the size of each ellipsoid to > have a 50% chance of finding the atom in that volume. This > shouldn't be > too hard but I'll let Eric tackle it if he has time. Hi David, This is one of those things that I'll endeavor to get into Chimera's production version of thermal ellipsoids, but that I can't spare the time for until then. My guess is that the eigenvectors/values of the U matrix are at the 50% probability level, but verifying that would require some research. If you do look into and find that that's not the case, just change the setting of the 'scale' variable of the start of the script to change the ellipsoid sizes to whatever size encloses 50%. --Eric

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suggestion/transform molecule coordinates
by Dougherty, Matthew T. 13 Jul '09

13 Jul '09

relating to the apply, close & help buttons 1)"reset" button The reset would remove prior transformations 2) "apply once" button. The apply once would function the same as a reset and apply in sequence. 3) display sum of current transformation (Euler & shift) Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

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Chimera-users July 2009