- Chimera-users - RBVI Mailing Lists

rmsd
by sdimicco 08 Nov '11

08 Nov '11

Dear Chimera developers, is it possible to calculate the rmsd between two proteins by the softwere? How can I do it? Thank you in advance. Simone

2 1

.transparency in bild format
by Keren Lasker 05 Nov '11

05 Nov '11

hello: I am trying to use the transparency option in the bild format. it seems that: .transparency 0.3 .sphere 0 0 0 10 results in a sphere however .color 1 0 0 .transparency 0.3 .sphere 0 0 0 10 results in a black image, it only works if transparency is set to 0. any suggestions what i am doing wrong? thanks, keren.

2 3

Adding sequences to an alignment
by Tom Goddard 02 Nov '11

02 Nov '11

Hi David, Here's the documentation on adding sequences to an alignment in Chimera http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu… It says it uses the Needleman-Wunsch algorithm with parameters you specify unless you have the "Simply append..." option enabled in which case it puts the sequence at the bottom with no gaps if the sequence has exactly the same length as the existing alignment. I guess you don't have Simply Append enabled. Probably Needleman-Wunsch is simply failing to align your new sequence to the existing alignment so it ends up putting it to the right of the existing alignment my inserting a huge gap at the beginning. How similar is the sequence you are trying to add to the alignment sequences? I'm not the Chimera expert on this topic (Eric Pettersen and Elaine Meng are) so I've posted to the Chimera mailing list so they can give you a better answer. Tom > Hi Tom, > My name is David and I'm a postdoc in Jack Johnson lab at Scripps. I'm writing as I've a question concerning the use of Chimera. > I've superimposed two structures in Chimera and generated a structure-based sequence alignement. I have two set of sequences (2 families) with a group associated with one of the two structures (and thus its sequence) and the other group being linked to the second structure. > I tried to extend the structure based sequence-alignement by adding new sequences and adding the first 2 sequences exactly did that i wanted: aligning them to the corresponding reference whose structure is displayed. > However when I add the other group of sequence, it doesn't result in aligning to the other sequence and instead add it after the overall alignment. > I'm sure that I'm missing something obvious, could you please help me sorting that out? > Thanks a lot > Best wishes > David > > David Veesler > Research Associate > The structural Virology lab - Johnson's lab > Department of Molecular Biology > The Scripps Research Institute > 10550, N. Torrey Pines Road > La Jolla, California 92037, USA > > >

2 1

Fwd: sphere viz in Chimera
by Elaine Meng 02 Nov '11

02 Nov '11

Begin forwarded message: From: Elaine Meng <meng(a)cgl.ucsf.edu> Date: January 8, 2008 10:09:06 AM PST To: Adam C Marko <adam.marko(a)ucsf.edu> Cc: Terry Lang <terry(a)lego.berkeley.edu>, sbrozell(a)scripps.edu, Eric Pettersen <pett(a)cgl.ucsf.edu>, Elaine Meng <meng(a)cgl.ucsf.edu> Subject: sphere viz in Chimera Hello, You guys will probably think I'm a nutjob (or prior suspicions may be confirmed), but Adam got me started thinking about how to improve sphere visualization in Chimera, and I wrote a short program akin to showsphere but that takes advantage of features in Chimera (attached at bottom - feel free to use, alter, redistribute, or ignore completely - I spot-checked the output but it's still caveat emptor). The old program showsphere was written in the time of Midas and shows the radii with a dot molecular surface. If you just show the PDB file with the sphere representation in Chimera, that doesn't include the radius information but just uses some default for carbon since the spheres are written as C atoms. The dot surface cannot be used for volume calculations in Chimera. Showsphere also made a separate file for each cluster. Chimera can show solid spheres, and an attribute assignment file can be used to set the radii from the SPHGEN output. Another difference from Midas is that you can read in multiple models from a single PDB file which are then separately displayable and specifiable. It was Adam's idea to take advantage of the controls in the Model Panel. So this new little program puts all the clusters (above a user-specified minimum size) into a single PDB file and creates an attribute assignment file for setting sphere radii in Chimera. The volume enclosed by a "molecular" surface around the cluster can be computed in Chimera. -- Example (using rec.sph, the SPHGEN output from the DOCK6 tutorial http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_… ): f77 chimerasphere.f -o csphere guanine.24% csphere enter name of sphere file: rec.sph rec.sph minimum size to include? 35 35 enter name of output PDB: recspheres.pdb recspheres.pdb enter name of radius assignment file: recspheres.rad recspheres.rad cluster # 1 contains 158 spheres cluster # 2 contains 80 spheres cluster # 3 contains 50 spheres cluster # 4 contains 46 spheres cluster # 5 contains 38 spheres -- then I started Chimera and used the following commands before saving screenshot below: open rec_noH.pdb (also from DOCK6 tutorial) open recspheres.pdb defattr recspheres.rad (to browse to this file instead, use "defattr browse" or Tools... Structure Analysis... Define Attribute. This step generates message "No attributes usable by Render dialog were defined" but that is nothing to worry about; just means "radius" is one of the attributes suppressed from appearing there) rep sphere #1 rainbow models #1 color purple #0 set bg_color white -- screenshot with Model Panel (Favorites... Model Panel) -- note you can toggle display of clusters individually using the Model Panel I originally had the program ask for a model number into which the sphere PDB file would be read, because the attribute assignment file must specify each sphere. For example, if you specified 2, you would have to "open 2 recspheres.pdb" and the assignment file would include specifications like #2.5:1017.het@c The current version doesn't ask and just uses specs like #.5:1017.het@c for which there is a [remote] possibility of matching something other than the sphere, but nonetheless it could happen. Lines for the alternative behavior are still in the file, just commented out. Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

2 3

docking sphere visualization
by Trent E. Balius 02 Nov '11

02 Nov '11

Dear Chimera-user list, I believe, currently, Chimera can not visualize docking spheres (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand) files directly, in order to do so, we need to create a pdb file of the spheres and then visualize them. It would be vary helpful for DOCK users if we could visualizes spheres directly from the .sph files produced by sphgen (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Sphgen) or sphgen_cpp. Radius and color information could then also be displayed. This might be a helpful new feature to be included in a future release of Chimera. Thank you, Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/

3 3

MD plotting
by Eric Pettersen 01 Nov '11

01 Nov '11

Hi all, For any of you using Chimera's MD Movie for trajectory playback, I just added the ability to plot atomic distances, angles, and dihedrals for your trajectory. You can click (or drag) on the plot to go to the corresponding frame. You create a plot by using the "Plot" submenu in MD Movie's Analysis menu. Most of the functionality is available in the current daily build, but tomorrow's build will have a couple of additional features: dumping plot values to a file, and showing the numeric value of the plot for the current frame in the list of plots (the value is blanked during playback since updating it slows down playback too much). Feedback welcome. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

alpha helix representation problem
by larif sofiene 29 Oct '11

29 Oct '11

greeting after a MD simulation of an in silico induced mutation A80P (located in an alpha helix) in a monomeric protein i get this strange alpha helix (a wire represented helix) http://imageshack.us/photo/my-images/573/alphahelix.jpg/ is it the induced mutation that break down the alpha 3 helix and disturb orientation of the helix axis or a problem with chimera not recognizing the helix (in sequence tool the helix is no more color filled as alpha helix after inducing mutation) thank you for this piece of art which is CHIMERA :)

2 2

managing CONECT table
by Francesco Pietra 27 Oct '11

27 Oct '11

Hello: In preparing a model comprising various fragments I would like to suppress from the PDB CONECT table two connections to the central transition metal. I wonder whether there are rules for such manipulations. Chimera detects (as a bond) only one of these two connections. thanks francesco pietra

2 1

Re: [Chimera-users] periodic box visualization
by Eric Pettersen 26 Oct '11

26 Oct '11

On Oct 26, 2011, at 4:52 AM, Giovanni Pavan wrote: > Dear all, > when a periodic system is visualized into Chimera (e.g., a periodic > waterbox), is it possible to visualize explicitly the borders of the > periodic box (defined for instance in the last line of coordinate/ > restart files in case of AMBER format structures)? > Last, is it also possible to see the periodic images of the original > box along X, Y & Z axes? How? > I thank you in advance for the support and I look forward to > receiving any feedback from you. Hi Giovanni, I'm sorry but neither of these is currently possible in Chimera. You'll have to use another visualization program (VMD?) if you need these capabilities. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

periodic box visualization
by Giovanni Pavan 26 Oct '11

26 Oct '11

Dear all, when a periodic system is visualized into Chimera (e.g., a periodic water box), is it possible to visualize explicitly the borders of the periodic box (defined for instance in the last line of coordinate/restart files in case of AMBER format structures)? Last, is it also possible to see the periodic images of the original box along X, Y & Z axes? How? I thank you in advance for the support and I look forward to receiving any feedback from you. Bye Giovanni Dr. Giovanni Maria Pavan SUPSI - Laboratory of Applied Mathematics and Physics (LaMFI) Centro Galleria 2, Manno 6928, Switzerland. e-mail: giovanni.pavan(a)supsi.ch skype: giovanni_pavan phone: +41 58 666 65 60

1 0

periodic box visualization
by Giovanni Pavan 26 Oct '11

26 Oct '11

Dear all, when a periodic system is visualized into Chimera (e.g., a periodic waterbox), is it possible to visualize explicitly the borders of the periodic box (defined for instance in the last line of coordinate/restart files in case of AMBER format structures)? Last, is it also possible to see the periodic images of the original box along X, Y & Z axes? How? I thank you in advance for the support and I look forward to receiving any feedback from you. Bye Giovanni

1 0

Fwd: Re: Upgrade your video/graphics driver. hirose
by Greg Couch 25 Oct '11

25 Oct '11

Forgot to send reply to the list. -------- Original Message -------- Subject: Re: [Chimera-users] Upgrade your video/graphics driver. hirose Date: Tue, 25 Oct 2011 15:02:04 -0700 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: HIROSE Junzo <hirose(a)fupharm.fukuyama-u.ac.jp> This is a common error with Intel integrated graphics and older Intel graphics drivers. The solution, if your system is new enough, is to go to the system vendor's website support pages and download (and install) the graphics driver update. Sometimes the graphics driver is referred to as a video driver. Good luck, Greg On 10/24/2011 03:14 AM, HIROSE Junzo wrote: > Dear Sir > > Side View doesn't work. I got the following command in Side View. > > > Unable to share graphics data with main window. > Upgrade your video/graphics driver. > > > How can I resolve this problem? > > > Dr. Junzo HIROSE > > > ****************************************** > > Fukuyama Univ. > JAPAN > > TEL 084-936-2111 > Email: hirose(a)fupharm.fukuyama-u.ac.jp > > **************************************** > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

Question
by Anna Starus 25 Oct '11

25 Oct '11

Hello, I am having difficulty to depict some bonds as solid lines or some as dashed lines for the bonds that are coordinated to the metal. For some reason when I changed one bond to dashed all of the bonds also change to that. How could I ungroup the coordinating bonds to the metal and be able to make some of them dashed and some solid? I would greatly appreciate the help. Thank you, Anna

2 1

delegate
by Zoe Cournia 24 Oct '11

24 Oct '11

Hello, I am trying to use the "delegate" command from the Midas program in Chimera, but the error message I get is that "delegate is not yet implemented". Is there an available "Extension Mechanism" in chimera? If not, is it possible to get the source code for Midas in order to compile it and use it with delegate? Thanks a lot for any help. Best Zoe -- ------------------------------- Dr. Zoe Cournia Investigator - Lecturer Level Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece zcournia(a)bioacademy.gr Office: +302106597195 Lab: +302106597568 Cell: +306944223123 -------------------------------

2 2

Error: Cannot write preferences file:
by Andrew Voronkov 24 Oct '11

24 Oct '11

Dear Chimera users I have problems with preferences file and actually when I run command line for example I instantle get the message: Cannot write preferences file: C:\Documents and Settings\avoron\Application Data\.chimera\preferences Maybe that is some problem with netowrk rights or security options and setup as far as reinstallation doesn't help. Best regards, Andrew

2 2

Upgrade your video/graphics driver. hirose
by HIROSE Junzo 24 Oct '11

24 Oct '11

Dear Sir Side View doesn’t work. I got the following command in Side View. Unable to share graphics data with main window. Upgrade your video/graphics driver. How can I resolve this problem? Dr. Junzo HIROSE ****************************************** Fukuyama Univ. JAPAN TEL 084-936-2111 Email: hirose(a)fupharm.fukuyama-u.ac.jp ****************************************

1 0

Cavities/Pockets
by George Tzotzos 22 Oct '11

22 Oct '11

I'm wondering if there's a way to work out the relative hydrophobicity of pockets/cavities of related receptors. Fetching CASTp IDs and rendering the surfaces of the cavities gives a crude idea of hydrophobicity of a given cavity. However, I'm looking for something that goes beyond visualisation. Any ideas would be most welcome. Best regards George

2 1

protein sequence editing at sequence level
by frederick lee 21 Oct '11

21 Oct '11

hello chimera users, i know how to add or delete an entire sequence entry, but i can't figure out how to delete a portion of a sequence entry or a set of aligned sequences. currently, i have to go to another program (e.g., jalview) to accomplish that. is there a way to do that within chimera? also when i edit a protein structure (e.g., remove chains) and save the resulting structure, the sequence information of the *original* structure is kept in the pdb file. is there a way to only save sequence info corresponding to the structure actually saved? thanks much in advance. fred (relatively new chimera user)

2 1

sym complains group t parameters
by Joe Ping-Lin Hsiao 21 Oct '11

21 Oct '11

Hi, I found an online post about how to use the sym command to duplicate models. The post is here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-June/006433.html The commands in the post are: open 1ei3 sym #0 group t,5,280 axis 1,0,.4 coord #0 surf true I got an error of "Invalid symmetry group syntax "t,5,280"" from the sym command. The versions that I have are daily build Oct 18 on Mac, and Oct 13 on Windows. Thanks, Joe

3 2

split segmented map
by Gabor PAPAI 21 Oct '11

21 Oct '11

Dear chimera team, I've found the map segmentation tool very useful. However I would like to split the map according to the segments. Is it possible to do that? Thanks in advance! Best regards, Gabor ----------------- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748

3 2

how to run the command line chimera without actually opening the GUI
by nurul 20 Oct '11

20 Oct '11

Hello, I have two structures to superimpose using the match command in chimera. Once the structures are matched, I save the two models in one pdb file. I can then just view this pdb file whenever I want. My question is: can I somehow just do this using the terminal? Meaning the graphic of chimera doesn't launch, but I get the pdb file that has the correct rotation matrix of the two superimposed structures. I don't have much programming experience, and I have no knowledge of calculating rmsd. Would appreciate if someone would pinpoint me where to start. Thanks.

4 3

.prmtop/.dcd combination for movie
by Francesco Pietra 20 Oct '11

20 Oct '11

Hello: I am running parm7 amber files with namd, thus having a .prmtop file and a .dcd file. Is there any possibility of having such a melange treated by movie? thanks francesco pietra

2 2

problem in coloring a selected region
by Manish Manish 20 Oct '11

20 Oct '11

Dear Chimera Developer, I want to select a region in protein molecule and then color. I have open a pdb file 1HA0 (attached), and then select a sequence TQNGGSNACKR (attached image) then color in blue (attached image). But this colors non selected part. I am using ubuntu 11.04 natty, VGA compatible controller: Intel Corporation Core Processor Integrated Graphics Controller (rev 18) Subsystem: Dell Device 0447 Kernel driver in use: i915 Kernel modules: i915 and Chimera 1.5.3 . Regards Manish

4 5

Labelling helices
by George Tzotzos 19 Oct '11

19 Oct '11

I've been looking at the documentation to find a way to number (label) protein helices. Perhaps I didn't use the right keywords so I didn't find anything helpful. What I would like to do is give ascending numbers to individual protein helices starting from the aminoacid terminus onwards. Any suggestions will be greatly appreciated. Regards George

2 1

Display misconfiguration error
by Enrico Morelli 19 Oct '11

19 Oct '11

Dear all, after the update to the latest version of chimera, in some machines I receive the error: Display misconfiguration. Please increase the color quality (24bit color or grater), update your display (graphics) driver, ....... I've a lot of workstation with the same graphis cards (Nvidia Quadro) and the same operating system (ScientificLinux 5). I didn't do anything except upgrade chimera. The previous version works fine on all PCs, and the new one in some PCs give me the display misconfiguration. I checked the PCs where the chimera doesn't works, all has the Nvidia drivers working in 24bit mode and with graphic acceleration enabled. So, I don't know how can solve the problem. Someone can help me? Thanks -- ------------------------------------------------------------------- (o_ (o_ //\ Coltivate Linux che tanto Windows si pianta da solo. (/)_ V_/_ +------------------------------------------------------------------+ | ENRICO MORELLI | email: morelli(a)CERM.UNIFI.IT | | * * * * | phone: +39 055 4574269 | | University of Florence | fax : +39 055 4574253 | | CERM - via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY | +------------------------------------------------------------------+

2 1