- Chimera-users - RBVI Mailing Lists

Electrostatic coloring on slice surface
by Tom Goddard 20 Mar '07

20 Mar '07

Hi Boaz, When you color a surface (e.g. GRASP surface) using electrostatic potential with the Surface Color tool it does show the correct colors on the slice if you are clipping the surface. This is described in the guide to volume data display http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorc… The colors are only assigned at the triangle vertices of the slice surface which can be seen by switching to "mesh" display in the Surface Capping dialog. To get finer resolution coloring increase the "Mesh subdivision factor" in the Surface Capping dialog from 1.0 to say 3.0 (giving ~9x more vertices). Press the Enter key after changing the number to see the effect. Tom Boaz Shaanan wrote: > Hi Tom, > > Thanks a lot. While we're at it I have another question related to > surface rendering. In the 'colour surface' window there is button that > says 'colour sliced ...'. Does that mean that if I covered a molecule > with surface and mapped a Delphi calculated potential map onto it, if > I then slice into the molecule, the surface covering this slice will > show the potential correctly ? That would be very nice but I'm just > wondering whether I can believe what I see. Grasp used to do this > nicely but I'd like to use chimera (and grasp is dead anyway as far as > I'm concerned - I don't have SGI's). I'd appreciate your input. > > Cheers, > > Boaz

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Re: [Chimera-users] pdb-l: structure based sequence alignment
by Eric Pettersen 16 Mar '07

16 Mar '07

Hi Sona, Before getting to your question, just wanted to mention that the post you quoted isn't accurate anymore: Chimera can incorporate structureless sequences into alignments as of the last production release (October). Once you have a structure-based alignment (or any alignment really) showing in Multalign Viewer you can add sequences to it using MAV's Edit menu. I don't know of any non-madness-inducing way in Chimera of superimposing 50+ ligands without writing a script. There are two kinds of scripts you could write. One is a text file containing the exact same commands you would type at Chimera's command line. You would give the file a suffix of .com or .cmd and open it using File...Open or the "open" command. The other type is a Python script, also a text file, which requires a little bit of learning but offers the ability to use loops -- quite helpful in this scenario. A Python script file would have a .py suffix and can be opened the same way as a Chimera-command script. For purposes of the example scripts below, I'm going to assume the ligands have the same residue name (FMN in the example), that there is only one occurrence of the residue per file, and the ligand atoms have the same name. PDBs you want to use that don't match these criteria you could do by hand -- hopefully there would just be a few. On the assumption that you have a mix of NMR and crystallographic structures, the script will delete hydrogens, yielding a heavy-atom only RMSD (probably a good idea anyway if there are any methyl groups). Lastly, I'll assume you have a reference structure to match onto already open in model #0 before you run the script. The Chimera-command script would be something like this: open 1jhf; del H; match #1:FMN #0:FMN; close 1 open 1kef; del H; match #1:FMN #0:FMN; close 1 open 1rd9; del H; match #1:FMN #0:FMN; close 1 etc. For the Python version I'll make one further assumption: that you have the PDB IDs listed in a file named "pdbs". The Python version would be: from chimera import runCommand # use runCommand to execute Chimera commands f = open("pdbs", "r") # open file containing PDB IDs for line in f: # read through file pdbID = line.strip() # remove trailing newline from text runCommand("open " + pdbID + "; del H; match #1:FMN #0:FMN; close 1") f.close() # close file The indentation for the lines that follow the "for" statement indicate that they are to be executed as the loop. The lack of indentation for the f.close() indicates that it is not part of the loop -- it is executed once the loop finishes. --Eric On Mar 15, 2007, at 6:54 PM, Sona Vasudevan wrote: > Hello Eric, > > Have a few questions about Chimera. I would like to superimpose > just the ligands bound to complexes. In this case I would like to > basically get a rms deviation of 50+ ligand co-ordinates (same > ligand from different PDBs). I now Chimera's match could do it but > is there a way a easier way to superimpose ligands? > > Thanks! > > Sona > > > On 2/6/06, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Sona, > UCSF Chimera (www.cgl.ucsf.edu/chimera) can certainly > construct a > structure-based sequence alignment, but can't incorporate > structureless > sequences into the alignment so maybe it's not what you're looking > for. > But just in case, here are the URLs for Chimera's Match->Align tool > (which creates the alignment) and MatchMaker tool (which superimposes > structures): > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/ > matchalign.html > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ > matchmaker.html > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab >

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Problems using Collaboratory
by slaton 14 Mar '07

14 Mar '07

Hi, Having some problems using Collaboratory mode. Some scenarios: 1. When attempting to host a collaboratory session between linux hosts on the same subnet, with another linux box running the hub, no one can join the session. I get the error connecting that suggests checking your firewall settings. None of the machines have iptables running, and since they are on the same subnet that should rule out border router/firewall issues. 2. If using a Mac OS X machine (PPC) to run the hub -- on a different subnet than the linux boxes, but within the same building -- the first linux box can join the hub. A second linux box on the same subnet fails with the same error as in 1) above. This can be replicated every time. Neither linux boxes are running iptables or any other firewall, they have nearly identical hardware and are running the same distro/version/patchlevel. 3. If the MOSX box (where the hub is running) now joins the session with the 1st linux box, they can chat with each other and see either others' pointers. However if the connected user on the linux box opens a model (for my tests, i used a SPIDER volume), the connected user on the MOSX box cannot see it. An error pops up on the linux box reading: "Error processing trigger: "Camera": AttributeError: '_chimera.Camera' object has no attribute 'viewDistance' Rotating/moving the model on the linux box triggers this error on the MOSX box: "Error processing trigger: "collaboratory": ValueError: unopen model Additionally, while sending chat messages from the MOSX box works, it also throws errors like this: "Error processing trigger; "Chat command": TclError: invalid command name ".38462968.47381600.47395144.47395584....[etc] 4. If i reverse scenarios here -- hosting on Linux and joining from MOSX (and the host machine) -- the results are nearly the same. Each user can chat and see the other's cursor, but as soon as one user loads a model it starts throwing errors like the ones mentioned above. After which, chat mode no longer works. So.....any known problems with collaboratory in this release, or any tips on troubleshooting these problems? All tests were performed using Chimera snapshot release 1.2352, i386 version (linux) and X11 version (MOSX). thanks slaton Slaton Lipscomb Nogales Lab, Howard Hughes Medical Institute http://cryoem.berkeley.edu

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Re: [Chimera-users] Chimera - Question
by Elaine Meng 13 Mar '07

13 Mar '07

Hi Peter, No problem - the features are documented, but there is no tutorial that includes adding a sequence. I tested the following with the most recent snapshot (1.2352, March 2007). (1) Open your sequence alignment in Chimera. I just found the following problem when testing the procedure: *if you created the sequence alignment with Match->Align, it is necessary to save it to a file (File... Save As from the Multalign Viewer menu, pick any format), quit from the alignment, and reopen it in Chimera (File... Open in the main menu) before you can add a sequence to it* ...this will be fixed in the next release, however. If the sequence alignment was already read from a file, no extra step is needed. (2) Choose "Edit... Add Sequence" from the Multalign Viewer menu and paste the new sequence in the dialog. Enter a name for the sequence, adjust the alignment parameters as desired, and click OK. Look at the alignment and decide whether it seems reasonable. If not, you can use "Edit... Delete Sequences/Gaps" to remove the sequence and try realigning it with "Edit... Add Sequence" and different alignment parameters. For example, if the sequence is fairly distantly related to the others, you may have better luck with blosum-30 than blosum-62. Editing is described here http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/multalignviewer.html#editing (3) If they are not already open, open one or more structures that associate with the sequence alignment. (4) Once your new sequence is aligned with the others to your satisfaction, you can draw out boxes on the alignment using the mouse. If the boxes enclose parts of the sequence(s) that are associated with the structure(s), the corresponding parts of the structures will be highlighted (selected). Or, you can go the other direction by selecting parts of the structures and seeing where they are in the alignment. These forms of crosstalk are described here http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/multalignviewer.html#crosstalk and in the "Sequences and Structures" tutorial. You can also show the secondary structure assignments on the alignment with "Structure... Secondary Structure... show actual" (for those sequences associated with structures) or "show predicted" (for sequences without structures) Alternatively, if you already have a sequence alignment that includes your sequence of interest plus others that will associate with structures, you can just open them all in Chimera and skip straight to #4. Sometimes I get alignments from databases such as Pfam. I hope this helps, 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 On Mar 13, 2007, at 2:27 PM, Peter Murphy wrote: > Thanks for the quick response Dr. Meng, > > Thanks to your helpful tutorial, I now know how to align two > structures and get an alignment. But I am interested in the ability > to add a sequence (that > doesn't have a structure) to the alignment and see if/where parts > of it map onto the structures. Is there such a tutorial on your > website, or might you be able to give me a quick rundown :P > > Thanks again > > -- > Peter Murphy, B.Sc., M.Sc Candidate > Atlantic Research Center > Dalhousie University > Halifax, Nova Scotia, > Canada

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Chimera - Question
by Peter Murphy 13 Mar '07

13 Mar '07

Hi, I have a quick question about your program. Normally (on a day to day basis) I use fairly basic features of chimera (coloring, etc) to produce pictures of crystal structure images (for presentations, papers, etc). Rarely do I have to use the more advanced features of chimera (Solvent accessible surface area, distance calculations, etc) so I don`t have a good idea of the limits of your program. Thus, I figured I would check to see if what I wanted to do is out of the scope of your program. I have a few crystal structures which I want to align (I now understand how to do this based on your online tutorial (thanks)), but what I really want to do is feed a third structure into the consensus structure (or if there is no consensus structure, just feed a known sequence into a known crystal structure to see if the sequence could form that structure. Is there anyway to do this in your program.. Thanks for any help you may be able to provide, -- Peter Murphy, B.Sc., M.Sc Candidate Atlantic Research Center Dalhousie University Halifax, Nova Scotia, Canada

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Rotated density maps
by Thomas Goddard 13 Mar '07

13 Mar '07

I added two Chimera commands "newmap" and "addmaps" that allow extracting a rectangular piece of a density map with axes that are rotated relative to the original map. http://www.cgl.ucsf.edu/chimera/experimental/resample_map/resamplemap.html This is useful for extracting substructures from electron microscope tomograms. It is not part of current Chimera distributions but can be obtained as a separate plug-in from the experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html It is called "Resample Map Commands" on that web page because data values from the original map are interpolated (i.e. resampled) on the new rotated grid. Tom

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~longbond
by Boaz Shaanan 12 Mar '07

12 Mar '07

Hi, I'm trying to use ~longbond to hide a long bond in the Calpha trace of a model (270-280 in ijsc_a) but the bond refuses to disappear. The bond is not there when atoms are shown in full and only shows up in the Calpha trace (atoms->show chain trace). I type ~longbond in the command line after the trace is on and nothing happens. What am I missing ? I'd appreciate your advice. Thanks, Boaz Boaz Shaanan, Ph.D. Associate Professor Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Re: [Chimera-users] independent movement
by Elaine Meng 12 Mar '07

12 Mar '07

Hi Michel, namesel is a newer command added after version 1.2304 - get the recent snapshot to use this command: http://www.cgl.ucsf.edu/chimera/download.html#snapshots The release notes for this snapshot list what has changed since 1.2304: http://www.cgl.ucsf.edu/chimera/1.2349/docs/relnotes/snapshot.html The links I included in previous messages were to "development" documentation, which will always be newer than what you have (although mostly the same if you have a recent version). The documentation included with a download is more synchronized - you can access and search your local copy of the documentation using the Chimera Help menu. ----- 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 On Mar 11, 2007, at 3:32 PM, michel dedeo wrote: > Elaine and Tom > > Thanks for your help! Savepos and reset will let me do exactly what I > want. It is good to know there are two selection commands as well. > > I have one more question. I can name a selection using the menu but > when I try to use the 'namesel' command I get an error: Unrecognized > command: "namesel". Does this command still exist? > > I am using production version 1 build 2304 2006/10/23 on Windows. > > Thanks again, > > Michel Dedeo > > > On 3/9/07, Tom Goddard <goddard(a)cgl.ucsf.edu> wrote: >> Hi Michel, >> >> I think Elaine's suggestion about using the savepos and reset >> commands >> is the best approach. >> >> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html >> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html >> >> >> The "movemodel" command envisioned in a previous mailing list entry >> >> http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-June/000843.html >> >> does not exist. I think I would make two simpler commands if some new >> ones were needed that look like: >> >> spin #1 0.3 0.4 0.5 90 20 >> >> (spin model number 1 about axis (.3,.4,.5) by 90 degrees over 20 >> frames) >> >> slide #1 5.2 8.2 3.1 20 >> >> (translate model number 1 by (5.2,8.2,3.1) over 20 frames). These >> would >> work in screen coordinates by default. But using local coordinates of >> the model or local coordinates of a second model would also be handy: >> >> spin #1 0.3 0.4 0.5 90 20 local #2 >> >> (spin about axis specified in local coordinate system of model #2) >> >> slide #1 5.2 8.2 3.1 20 local >> >> (translate with vector specified in local coordinates of the model). >> >> These local coordinate versions allow the motion to stay the same >> if you >> rotate the whole scene. Neither the spin nor slide command currently >> exists. There are move, turn, and roll commands in Chimera that have >> more limited capabilities, only allowing rotation axes and shifts >> to be >> x, y, or z screen axes. >> >> Tom >> >> >> >> >> >> >>

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Re: [Chimera-users] surface display
by Tom Goddard 10 Mar '07

10 Mar '07

Hi Markus, This is a problem with the surface calculation library MSMS used by Chimera. It crashes on specific PDB files. It is described more in this post: http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-February/000685.html which suggest you use Chimera command vdwdefine * * +0.01 to make the atom radii 1/100 Angstrom bigger which may circumvent the crash. Trying to surfce fewer residues generally does not fix the problem because Chimera still computes the whole surface and then just limits the display to the few residues you selected. Here is the Chimera bug report about this problem. http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=1295&database=chime… Tom Markus Voehler wrote: > Tom > > I have installed the new version and the same thing happens. Here is > what I do: > 1) open pdb (3003 atoms) > 2) display round ribbon, hide atoms/bonds > 3) action --> surface --> show also tried it on a smaller selection of > a few residues. > > I have submitted the chimera error report and have attached the crash > report. Any ideas would be appreciated. > > Markus > > > On Mar 9, 2007, at 1:43 PM, Tom Goddard wrote: > >> Hi Markus, >> >> Is your problem with molecular surfaces (menu Actions / Surface / >> show) or contour surfaces of volume data? >> >> In either case you should first try a newer version of Chimera. I >> recommend trying the snapshot 1.2352 released this week (scroll down >> the Chimera download page a little). >> >> http://www.cgl.ucsf.edu/chimera/download.html >> >> Tom >> >

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viewing VRML files in chimera
by preethi＠bu.edu 10 Mar '07

10 Mar '07

Hi, I used an SGI compiled "ivtovrml" program to convert a .iv file to .wrl file in order to view it in Chimera. I got an error, not in VRML97 formatError near line 1: and this was repeated a few times. Is there any other program that is available to convert it to the right VRML format readable by Chimera? I did a little searching on the web and coudnt find one. Thanks in advance, Preethi.

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