April 2010 - Chimera-users - RBVI Mailing Lists

why is Chimera so slow?
by Scott Classen 14 Apr '10

14 Apr '10

Hi All, First off, I'm fairly new to Chimera, and so far I'm very impressed with the functionality. Thanks for the great tool. I am embarking on a fairly intensive comparison of a dozen or so structures and I'm running into some serious performance issues. I have an older Mac Pro with dual 2.66GHz Intel Xeon processors, 14GB RAM, ATI RadeonX1900 w/512MB VRAM and Chimera (1.4.1 build 30365). I've got 3 PDBs loaded up and have calculated surfaces for all three with a vertex density of 20 (perhaps too high? but I need accurate values for the solvent-excluded surface for particular residues). With 2 models and 2 surfaces things start to slow down a bit, but are manageable. With 3 models and their associated surfaces I can't even rotate the view at all. Even if I only show one residue and residues with 5A. It's as if Chimera is doing all the behind the scenes calculations to rotate all the surface triangles and atomic coordinates that aren't even being displayed. Is there something I'm missing? Is it it unrealistic to set my surface density to 20? Any advice? Thanks, Scott

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X-server segmentation fault on launching chimera
by Francesco Pietra 14 Apr '10

14 Apr '10

Hello: Having upgraded Debian Linux i386 squeeze release from kernel 2.6.30 to 2.6.32 everything works except X-server segmentation fault on launching CHIMERA, build 30282 of last March 29. I have successfully recompiled CHIMERA, last Apr 14 build, on the updated Linux release, to no avail. I need the experimental builds for features not included in the stable release (centroid trace in movie). To compare, another graphic program, GIMP, can be launched correctly. Below - between *** - the final part of "Xorg.0.log" reporting troubles. Before that, the log is identical to when X-server is working properly. Thanks for suggestions. francesco pietra ********* Backtrace: 0: /usr/bin/X (xorg_backtrace+0x3b) [0x80ada5b] 1: /usr/bin/X (0x8048000+0x5aa75) [0x80a2a75] 2: (vdso) (__kernel_rt_sigreturn+0x0) [0xb78b240c] Segmentation fault at address (nil) Fatal server error: Caught signal 11 (Segmentation fault). Server aborting Please consult the The X.Org Foundation support at http://wiki.x.org for help. Please also check the log file at "/var/log/Xorg.0.log" for additional information. (II) Power Button: Close (II) UnloadModule: "evdev" (II) Power Button: Close (II) UnloadModule: "evdev" (II) AT Translated Set 2 keyboard: Close (II) UnloadModule: "evdev" (II) ImPS/2 Logitech Wheel Mouse: Close (II) UnloadModule: "evdev" ********

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Fwd: Re: install
by Greg Couch 13 Apr '10

13 Apr '10

Forgot to cc the list. -------- Original Message -------- Subject: Re: [Chimera-users] install Date: Tue, 13 Apr 2010 11:25:43 -0700 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: Jay Brown <jcb2g(a)virginia.edu> It may be that you downloaded the 32-bit version but only have the 64-bit runtime libraries installed or vice-versa. If you run "uname -m" in a terminal, it should print x86_64 if you have a 64-bit version of Linux. Please send me the full error message and I may be able to say more. - Greg On 04/12/2010 01:13 PM, Jay Brown wrote: > > Dear Chimera-Users: > > I am trying to install Chimera on a Linux Fedora 12 computer. Download > goes OK, but when I try to install the program I get an error message > saying: bad ELF interpreter: No such file or directory > > Do you know what this means? I can't find anything about ELF interpreter. > > -Jay Brown > > Jay C. Brown > > Department of Microbiology > > University of Virginia School of Medicine > > 1300 Jefferson Park Ave. > > Charlottesville, VA 22908 > > Email: Jcb2g(a)virginia.edu > > Phone: 434-924-1814 > > http://people.virginia.edu/~jcb2g/index.htm > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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xfowarding not working in new chimera
by Kenneth Frankel 13 Apr '10

13 Apr '10

My older version of chimera x forwards with no problem; from the about ucsf chimera window its beta version 1 build 2064 2004/12/15 for linux2 We have upgraded the 32 and 64 bit version which run fine locally. but when we run from another computer with ssh either with -X, -Y, -XY , -o ForwardX11=yes frankel@graphics1 we always get a crashe after trying to do something (e.g fetch a pdb) with the same genral error message frankel@graphics1:/home/frankel 102% /programs/chimera-1.4.1-x86_64/bin/chimera X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 144 (GLX) Minor opcode of failed request: 181 () Serial number of failed request: 5374 Current serial number in output stream: 5379 (serial numbers may differ between runs) Can this be fixed? (We suspect it's a mesa library problem). Also when running nx client, even the old version of chimera from crashes. I'll have to get the error message later, but does anyone have experience running over nx client? we've gotten pymol, and vmd to work. thanks Ken Frankel

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Re: [Chimera-users] Chimera-users Digest, Vol 84, Issue 12
by Chinthaka Silva 13 Apr '10

13 Apr '10

Hi, Is there a way to quantify the electron densities in a unit cell with UCSF? Thanks, Chinthaka. On Tue, Apr 13, 2010 at 2:08 PM, <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. install (Jay Brown) > 2. Re: Analysis of dihedral angles (Eric Pettersen) > 3. Re: Analysis of dihedral angles (sette(a)uniroma2.it) > 4. Re: Analysis of dihedral angles (Elaine Meng) > 5. Re: Analysis of dihedral angles (Eric Pettersen) > 6. Re: Display a spider volume data in a specific orientation > (Tom Goddard) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 12 Apr 2010 16:13:27 -0400 > From: "Jay Brown" <jcb2g(a)virginia.edu> > To: <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] install > Message-ID: <009501cada7c$9ccfe2b0$d66fa810$@edu> > Content-Type: text/plain; charset="us-ascii" > > Dear Chimera-Users: > > I am trying to install Chimera on a Linux Fedora 12 computer. Download goes > OK, but when I try to install the program I get an error message saying: > bad > ELF interpreter: No such file or directory > > Do you know what this means? I can't find anything about ELF interpreter. > > -Jay Brown > > > > Jay C. Brown > > Department of Microbiology > > University of Virginia School of Medicine > > 1300 Jefferson Park Ave. > > Charlottesville, VA 22908 > > > > Email: Jcb2g(a)virginia.edu > > Phone: 434-924-1814 > > http://people.virginia.edu/~jcb2g/index.htm > > > >

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Analysis of dihedral angles
by eduardo.troche＠uvigo.es 13 Apr '10

13 Apr '10

Hi all, I'm a new Chimera user. I'm performing some molecular dynamics with a more or less simple system with Amber,and now that I have them done, I would like to analyze some specific data,like changes in a dihedral angle during the dynamic process, or distances between pairs of atoms. If I select several dihedral angles in Chimera and I play the dynamic movie, I can see these changes, but is it possible to get a table of results that shows the value of this angle for each step of the dynamic process? Thank you every body! Eduardo

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surface holes
by Eric Pettersen 12 Apr '10

12 Apr '10

On Apr 12, 2010, at 5:05 AM, Guy Nimrod wrote: > Hello, > When I load complex structure (e.g., pdb 3mht) and show the surface > of one chain (e.g. selectchainA; action->surface->show), the > generated surface does not cover the interface between the query > protein and the other chains. Consequently, the interface appears as > a hole in the surface (see attached figure). > Is there an easy way to visualize the whole surface (i.e. the > generated surface on a selected chain will disregard chains which > are not selected)? Hi Guy, When you surface some subset of atoms in Chimera, Chimera still considers all atoms in the same "surface category" as the subset for purposes of computing the surface -- it just doesn't show the surface of the atoms not in the subset. So for example if you ask for a surface on a single residue Chimera doesn't make a surface that completely encloses the residue -- the surface is "open" where the residue connects to the rest of the molecule. Similarly, a single chain of a multi-chain molecule may not be completely enclosed if Chimera considers other chains of the molecule to be in the same surface category. That is what has happened here. Chain A (the protein) and the chains C and D (the nucleic acid) have been classified into the same surface category (main). To get the enclosed surface that you want you need to put chain A into a surface category of its own and surface that. These two commands will accomplish that: surfcat prot :.a surf prot The surface actually inter-penetrates the nucleic acid because of the flipped-out base, like this: --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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question about ViewDock
by Miriam Gochin 12 Apr '10

12 Apr '10

I have a question about ViewDock. It works fine for one receptor and several ligands, but if I open a second receptor model and rotate it, then ligands I open with ViewDock for the second receptor are in the original (unrotated) position. Is there a way to correct the ligand positions for the current rotation? Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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install
by Jay Brown 12 Apr '10

12 Apr '10

Dear Chimera-Users: I am trying to install Chimera on a Linux Fedora 12 computer. Download goes OK, but when I try to install the program I get an error message saying: bad ELF interpreter: No such file or directory Do you know what this means? I can't find anything about ELF interpreter. -Jay Brown Jay C. Brown Department of Microbiology University of Virginia School of Medicine 1300 Jefferson Park Ave. Charlottesville, VA 22908 Email: Jcb2g(a)virginia.edu Phone: 434-924-1814 http://people.virginia.edu/~jcb2g/index.htm

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problem with new Chimera 1.4 and 1.4.1 OSX Aqua
by Miriam Gochin 10 Apr '10

10 Apr '10

Dear Chimera team, I am not sure what I am doing wrong, but the new version does not open correctly on my Mac (OS-X-10.6.2). I get a small black square surrounded by white space that will not enlarge. Is there some setting I should adjust? Best wishes, Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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Chimera-users April 2010