- Chimera-users - RBVI Mailing Lists

level of detail (vrml)
by Damien Larivière 22 Apr '10

22 Apr '10

Dear all, Chimera is able to display VRML file. Is it able to display VRML file containing level of detail? (My first tentative was not a success but I do not think the file I used respected the format convention). My best reagrds Damien

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Small molecule dimensions
by le monk 21 Apr '10

21 Apr '10

Hello, I have a few pdb files of small molecules that I would like to know the dimensions of. Is it possible to use Chimera the measure the minimum x y z lengths - taking into account Van der Waals radii? Or perhaps you could suggest other software for this? Many thanks _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ Do you have a story that started on Hotmail? Tell us now

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hide dust
by weimin wu 20 Apr '10

20 Apr '10

Sometimes after we remove the dust using the tool of hiding dust, we want to save the map directly instead of using command "mask #0 #0" to generate a maskfile. The reason is that the masked map has minimized map size and different with original one. Even after we recover the map size and origin, it always has half pixel issue, and if we apply this mask to original map, the output will have some masking artifact. The iso-surface of the output will not be as smooth as original map or the map after hiding dust. weimin

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Chimera on Acer Aspire 1410
by Mario J. Borgnia 20 Apr '10

20 Apr '10

Hi, I am running Chimera chimera-1.4.1-linux_x86_64 on my "netbook" style Acer Aspire 1410 with the following specifications: OS: Linux 2.6.31.12-0.2-desktop x86_64 Processor: Intel(R) Celeron(R) CPU 743 @ 1.30GHz Intel Mobile GM45 Express Chipset 1366x768 pixels The program runs well but surfaces disappear upon rotation. This is true for solid surfaces, as soon as I set the opacity to 0.99, the surfaces are no longer affected. Any hints? Thanks Mario Borgnia

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Chimera and Nvidia 3D vision
by Joern Lenz 20 Apr '10

20 Apr '10

Hi there, I am wondering if anyone of you knows if I can use my Nvidia GTX295 together with the 3D vision glasses and a Samsung SyncMaster 120Hz screen to view 3D in Chimera using a Debian Lenny or a Windows 7 OS. About two years ago, Nvidia said they will support Unix systems with their glasses. However, up to now there is no news about that. Do you have any idea or even a way to get 3D on in Chimera using the hardware above ? Many thanks. Cheers, Joern

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Save session for movie
by Francesco Pietra 18 Apr '10

18 Apr '10

Hello: I am carrying out the analysis of MD for a ligand wandering through a protein. Specifically following the pathway through the trace left by the centroid of the ligand. Apparently the "save session" doe not work for movie. I.e., I stopped the movie (with the centroids drawn at the various steps) at a certain step, then "save session" destroyed the graphics and only alpha-numeric appeared on the terminal. Is there a diffent procedure for such a case or only "save image"? This would greatly limit what could be done by reorienting the protein, coloring, labeling, etc. thanks francesco pietra

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Is it possible to make ribbons transparent
by Ajith Harish 17 Apr '10

17 Apr '10

Hi, Please let me know if it is possible to make the ribbon representations transparent like the surfaces? Thanks, Ajith

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Space Navigator on Linux
by Daniel Luque 15 Apr '10

15 Apr '10

Dear all, I am trying to use a 3DConexion SpaceNavigator with chimera in my linux machine. I have installed the SpaceNavigator drivers and they work properly with the manufacturer test tools (xcube and xvalue). Althought I am running the last chimera release, when I open chimera it does not "see" the device. Should I do something special when I start chimera or once it is open in order to use the device? Thanks in advance, Daniel

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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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[Re: Residue exposition cutoff]
by Yasser Almeida Hernández 07 Apr '10

07 Apr '10

Thanks for your answer... About this i have an idea resumed in two question: In principle an solvent-exposed residue must have in average high value of b-factor, so will be very flexible. 1 - Can i say that those residues that have and average b-factor up to a cutoff value AND an areaSAS (or % of that area) superior than a other cutoff value, will be exposed to the solvent??? 2 - There is a cutoff value of b-factor for the residues flexibility? Best regards -------- Forwarded Message -------- From: Elaine Meng <meng(a)cgl.ucsf.edu> Reply-to: Chimera BB <chimera-users(a)cgl.ucsf.edu> To: Yasser Almeida Hernandez <almeida(a)cim.sld.cu> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Residue exposition cutoff Date: Mon, 5 Apr 2010 11:22:37 -0500 Hi Yasser, Actually you don't have to use DMS ... if you show a surface in Chimera it also automatically computes the SES (solvent-excluded surface) and SAS area per atom and per residue, attributes named areaSES and areaSAS. For more details, see these previous posts: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003291.html > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003597.html > Some notes about areaSES and areaSAS: (1) if you don't want to include inside bubbles in the surface area calculations, after creating the surface(s) remove the inside bubbles with the command: setattr s allComponents false (2) the surface that Chimera displays is the SES (also known as Connolly surface or molecular surface), not the SAS, although both sets of areas are calculated Actually Tom Goddard mentioned the areaSAS attribute briefly in an earlier reply to you: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/003995.html> As to what cutoff should be used for classifying atoms or residues as buried or exposed, I'm not aware of any commonly used value. It is a more philosophical issue that depends on your ultimate purpose. You might try coloring by different cutoffs to try to decide what is appropriate for your research (keeping in mind that the SES is what Chimera actually displays), or read publications of similar work to see what other researchers have used. In publications, I have seen residues classified by "fraction" or % of the surface area of a residue in the structure divided by the area of that same type of residue in a hypothetical fully exposed state, but I don't remember the exact cutoffs used, and Chimera does not provide the fully exposed values. An example of a program that does provide such values is GetArea: <http://curie.utmb.edu/getarea.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 On Apr 3, 2010, at 1:38 PM, Yasser Almeida Hernández wrote: > Hi all.... > I have 2 question, beyond Chimera's issues. > > 1 - There is some cutoff value to consider a residue or more > strictly, an atom exposed to the solvent?. > > 2 - Could i set a this cutoff using the area values and types (SR0, > SC0 and SS0) from the DMS program output? > > 3 - Wich program you recommend to compute SAS? > > Thanks, > best regards ----- Terminar mensaje reenviado ----- -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

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amino acid clashes
by Kirys, Tatsiana 06 Apr '10

06 Apr '10

Dear All, i'm trying to figure out scheme for calculating protein amino acid clashes. I've read in User's Guide that 1) The overlap between two atoms is defined as the sum of their VDW radii minus the distance between them and minus an allowance for potentially hydrogen-bonded pairs: overlapij = rVDWi + rVDWj dij allowanceij 2) It has an option: Ignore contacts of pairs [ N ] or fewer bonds apart (N=4 by default). i calculated rotamer clashes from "Penultimate rotamer library" according to 1) and there are clashes between N ans C N and CB N and CG CA and CG CA and OD1 etc. i'm sure i do something wrong because "Penultimate rotamer library" was checked for the clashes. I dont understand why 2) option exists, what is the physical meaning of it? and why N can be cosed arbitrary? many thanks Tania

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structural similarity measures in Chimera
by Elaine Meng 05 Apr '10

05 Apr '10

Dear Minming, Dr. Ferrin forwarded your question to me. We recently added calculation of structure similarity measures to Chimera. This capability is not in versions 1.4/1.4.1, but only in 1.5 (recent daily builds, which are also available from our download page). In such recent builds, the "Match -> Align" tool (under Tools... Structure Comparison in the menu) calculates two measures that have been described in previous publications, the SDM and the Q- score. The SDM has been used to construct phylogenetic trees before. I don't know if the Q-score has been used that way. Documentation for Match->Align and details of these measures: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchal… > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchal… > However, there are some issues that may affect whether you decide to use Chimera to calculate these values for your structures: (1) You would need to run Match->Align for each pair. There is no option to do all pairwise comparisons on multiple structures. You would need to script looping through all pairs (with python or shell scripting). (2) There is no Chimera command for Match->Align. Thus Match->Align would also need to be run via python. I don't have scripting expertise, so someone else would have to provide more details if you decide to try this. (3) Before you run Match->Align, the structures need to be superimposed. We purposefully made Match->Align independent of the superposition method. There are several possible ways to superimpose structures in Chimera, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> but probably the easiest in your case would be MatchMaker, which is also available as a Chimera command (matchmaker or mmaker, see that URL and links within). Usually the mmaker defaults work pretty well, for example Chimera commands: open 2mnr open 4enl mmaker #0 #1 (Then you could try running Match->Align interactively. The SDM, Q- score, etc. are reported in the Reply Log, opened with Favorites... Reply Log in the menu.) 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 P.S. we recommend sending Chimera questions to chimera-users(a)cgl.ucsf.edu (I CC'd that list here after removing the details from your original mail) > -------- Original Message -------- > Subject: A question about your software(UCSF Chimera) > Date: Tue, 23 Mar 2010 21:55:06 -0400 > > Dear Dr. Ferrin, > > I am very interested in using your software UCSF Chimera, which have > some > commands that can do the job of aligning and measuring a distance > between two > protein structures. > > I am a PhD student at Purdue University working on the evolution of > protein > structure with Professor Peter Waddell. I was hoping to use your > structure > alignment software to obtain a pairwise structure distance matrix. > This > matrix > will then be used in phylogenetic analyses, comparing the trees and > treeness > of that structural distance compared to that produced by other > published > methods. > [...] > Could you please tell me if your structural alignment software can > easily > produce a complete pairwise distance matrix for a list of ~50 > structures? I did > not see a way to do this. If not, is there any easy way to modify it > to > do this? > [...] > > Best Regards and Sincerely, > Minming Li >

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Residue exposition cutoff
by Yasser Almeida Hernández 05 Apr '10

05 Apr '10

Hi all.... I have 2 question, beyond Chimera's issues. 1 - There is some cutoff value to consider a residue or more strictly, an atom exposed to the solvent?. 2 - Could i set a this cutoff using the area values and types (SR0, SC0 and SS0) from the DMS program output? 3 - Wich program you recommend to compute SAS? Thanks, best regards -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

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Possible bug in Chimera RMSD calculation
by Yasser Almeida Hernández 03 Apr '10

03 Apr '10

Hi all.... In Chimera , i selected a single pair of atoms for RMSD calculation with the command rms (rms #1:221.A@NE #0:221.A@NE) and it return the distance between the atoms ???? It would be a bug??? Please check this.... Thanks -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 214-3178 almeida(a)cim.sld.cu ---------------------------------------------------------------- Correo FENHI

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Coloring model represented as PipesAndPlanks
by Ibrahim Moustafa 01 Apr '10

01 Apr '10

Dear Chimera team, I have a problem with coloring different regions of the protein presented as PipesAndPlanks. I know I can change the colors of the SS elements from the menu of PipesAndPlanks. But, this is not what I want: I want to color different regions of the protein with different colors and not to be limited with the colors given to the SS. Before, I had no problem in doing so. I think this problem appeared in the recent updates. Something I noticed and could be related is that to change the presentation from the default chimera to PipesAndPlanks the new presentation assigned the same model# as the original model. I think, in previous versions the new presentation used to be given a new model#. Similarly, if I want to create a map for the model using (molmap) it is given the same model # rather than a new model# as used to be. I run Chimera version 1.4.1 (build 30282) on a Mac OSX 10.4 (PPC). Thanks for help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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Daily build requirements
by sherden＠caltech.edu 31 Mar '10

31 Mar '10

So to get thermal ellipsoids to display from a .cif file (as opposed to a .pdb) it looks like I need version 1.50 or greater of Chimera, but it looks like versions of Chimera above 1.4x don't seem to run on my Mac (I have system 10.4.11). What OSX system version do I need so that I can run a version of chimera that I can get thermal ellipsoids to display from a .cif file? Or, conversely is there a way I can get one of the more recent daily builds to run on OSX system 10.4.11? --Nat (Nathaniel Sherden) California Institute of Technology

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