- Chimera-users - RBVI Mailing Lists

Two transparent models and memory leaks
by Thomas Goddard 22 Mar '07

22 Mar '07

C Akey report problems with display of two transparent models and excessive memory use and crashes when saving images. ------------ Tom- Sorry to bother you but I am having serious problems with Chimera while trying to make figures for a paper. After you fixed the sessions number problem, so that they are retained in the same numbered slots from one session to the next, I found that my most recent sessions made with this version, would not work properly when I wanted two different displayed volumes to have transparencies different from 1. This worked in earlier versions and then I started over with a new session, imported everything and it is working again. Maddening. If you have a ribbon within a volume and try to vary the transparency, it almost disappears instead of having a gradual blending effect (see attached figures A,D panels). I am using a PC under XP with 1Gb mem and 512 GB graphics card. I have checked and memory is not the problem. {However, if you quit a session then open another session, Chimera does not give the memory back to the system, so your memory use soars, YOU MUST QUIT BEFORE OPENING A NEW SESSION.} Here is another killer bug: When you record an image full screen, about half the time you get a fatal error in pythonw.exe, it wants you to contact Microsoft and then Chimera crashes losing everything. The error from chimera reads "failed 1073741891" but there is no chance to report the bug. So after battling to get to the point of recording images, the program quits on me about half the time. By the way, when Chimera is shown full screen on our new Linux machine, it doesn't clearly show all the icons on the left hand side of the screen, they are partly occluded. sorry about the bugs but its starting to get to me. cheers C Akey

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New Chimera molecular surface code
by Tom Goddard 22 Mar '07

22 Mar '07

Miguel Ortiz Lombardia asks when Chimera will be able to compute solvent accessible surfaces. -------- Original Message -------- Hi Tom, I would like to know if there has been any advancement in changing the surfaces code. I know you had plans to write your own so that chimera would not rely on msms, and I am very interested in this development because it would allow the use of solvent accessible surfaces apart from molecular surfaces. The former are more appropriate, among other questions, to map electrostatic potential maps (less local effects). I would be happy to test around, if you need testers. Unfortunately my programming skills are quite minimal. But I'll be patient anyway ;-) Thanks to all of you for this great tool! Cheers, Miguel

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MODELLER interface
by Elaine Meng 21 Mar '07

21 Mar '07

Hi Stefano, No arguments here - we have talked about it and I've expressed a need for it for years. The problem is that there are many other features that seem to be at least as high priority, and limited time and manpower available. To name only a few of the things in progress: energy minimization, morphing, interaction with dendrograms (along with sequence alignments), more display preferences, more animation commands, and producing ray-traced images. There is a "model loops" tool that interfaces with MODELLER, but it only produces alternate conformations of loops that are already in a structure. That was implemented because people in the MODELLER (Sali) group here wanted it the most, and it needs work - e.g. currently there is no convenient way to merge a chosen loop conformation back into the structure. Nevertheless, this is another important item and I will share your message to help ensure it does not fall off "the list." I imagine any validation tools would be farther down on the list than the interface for comparative modeling, although we do already have a tool that finds clashes and close contacts. Elaine On Mar 20, 2007, at 10:05 PM, Stefano Ciurli wrote: > Elaine, > > following our discussion on Chimera and DelPhi, and these recent > mails on modeling, don't you think that it would be nice to > interface Chimera to Modeller, as the latter one is one of the most > used software to do homolog modeling? The interface could be a sort > of way to funnel into Modeller the alignment and the structure of > the template(s) for Modeller to use and then read back into Chimera > the results of the modeling, with tools to establish the quality of > the model itself (I am thinking of Prosa, Procheck or WHATIF) > > Regards > Stefano > -- > ____________________________________________ > > Stefano Ciurli > Professor of Chemistry > Laboratory of Bioinorganic Chemistry > Department of Agro-Environmental Science and Technology > University of Bologna > Viale Giuseppe Fanin, 40 > I-40127 Bologna > Italy > Phone: +39-051-209-6204 > Fax: +39-051-209-6203 > > http://www.cerm.unifi.it > http://www.isa.unibo.it/ISA/ > > "Fatti non foste a viver come bruti, > ma per seguir virtute e canoscenza" > Dante Alighieri - Inferno - Canto XXVI > > "Ihr seid bestimmt, nicht Tieren gleich zu leben, > Nein, Tugend zu erringen und Erkenntnis" > "Ye were not form'd to live the life of brutes, > But virtue to pursue and knowledge high"

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sequence & structure in Chimera
by Elaine Meng 20 Mar '07

20 Mar '07

Hi Abhijit, If I understand correctly, there were two questions here: > One more question is it possible to take a protein sequence of a gene, > part of which is cloned, crystallized and 3d structure is available, > and superimposes the protein sequence with the reported crystal > structure? Or how can you model a protein sequence to generate a > putative structure, for the part that hasn’t been crystallized so far, In Chimera, (1) can you associate a structure with a sequence that is read in from a separate file? short answer: yes, if that sequence is in an alignment (2) can you do comparative modeling (create a 3D model of an unknown structure starting from a known structure that is thought to be similar)? short answer: no, except simplistic replacement of a few side chains with the command "swapaa" I'll start with #2: Chimera does not do comparative modeling or threading different sequences on a known structure. Besides the approaches mentioned by Eric (getting a model from MODBASE or using the MODELLER program to make the model yourself), listed below are several web servers that might be useful. I believe the first two replace side chains while the others perform more complete modeling (can handle insertions/deletions and adjust the backbone). It's been a while since I used any of these, however, so you should read any author-provided information. - SCWRL server http://www1.jcsg.org/scripts/prod/scwrl/serve.cgi - Maxsprout server http://www.ebi.ac.uk/maxsprout/ - ModWeb server (requires registration) http://alto.compbio.ucsf.edu/modweb-cgi/main.cgi - RAPPER server (registration encouraged) http://mordred.bioc.cam.ac.uk/~rapper/ - PSIPRED server http://bioinf.cs.ucl.ac.uk/psipred/ - Swiss-Model server http://swissmodel.expasy.org//SWISS-MODEL.html Now question #1. You already saw the Sequence tool, which shows the exact sequence of any peptide or nucleotide chains in structures open in Chimera. However, you might want to read in a sequence from a separate file and associate it with the structure to allow the same kinds of crosstalk (a selection on the sequence selects the structure and vice versa). You can do that, if you have an alignment of that sequence with one or more additional sequences. These other sequences don't need to have any structures, and your sequence of interest does not have to match the structure exactly to associate with it (often there are point mutations, or the sequence is for a close homolog of the structure, or the structure is missing a few residues here and there, or is only one domain from the whole sequence). Here's a list of the sequence alignment formats that can be read (you can just use File... Open in the Chimera menu): http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment and the "Sequence-Structure Association" section in this page may be useful: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/framemav.html 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

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Motion callback functions
by Tom Goddard 20 Mar '07

20 Mar '07

Hi Karin, I've attached some example Python code that monitors the motion of models in Chimera. It registers an OpenState trigger. For your case you might update the color on your plane when the plane moves but the map does not move. Let me know if more details would be helpful. Tom Karin Gross wrote: > Hi Tom, > > i have a question concerning rotation and translation of surface models in > chimera. > I want the user to be able to rotate/translate my plane via mouse, but run the > computation of coloring and do the coloring during the movement. > Is it possible to register a python callback for this, and get the > rotation/translation information? > > Thanks > -Karin > > # ------------------------------------------------------------------------------ # Example code that monitors the motion of models in Chimera. # # Each Chimera Model object has an openState attribute whose value is an # OpenState object. The OpenState object has attributes xform, active, # cofr (center of rotation), bbox (bounding box). These are defined in the # Chimera C++ header file OpenModels.h. (Chimera C++ headers can be downloaded # from http://www.cgl.ucsf.edu/chimera/sourcecode.html) # # This example code monitors changes in the OpenState objects for all models. # class Monitor_Motion: def __init__(self): from chimera import triggers h = triggers.addHandler('OpenState', self.xform_changed_cb, None) self.handler = h def xform_changed_cb(self, trigger_name, call_data, trigger_data): if 'transformation change' in trigger_data.reasons: # The transformation matrix of some model has changed. from chimera import openModels mlist = openModels.list() # All open models. for open_state in trigger_data.modified: models = filter(lambda m: m.openState == open_state, mlist) if models: names = ', '.join(map(lambda m: m.name, models)) print names, 'moved' print open_state.xform def stop_monitoring(self): from chimera import triggers triggers.deleteHandler('OpenState', self.handler) self.handler = None # ------------------------------------------------------------------------------ # mm = Monitor_Motion()

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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 13 Mar '07

13 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 09 Mar '07

09 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 09 Mar '07

09 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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surface display
by Markus Voehler 09 Mar '07

09 Mar '07

I have a PowerBook G4 and am not able to display surfaces on that laptop (it works fine on the SGI). I am running OSX 10.4.8 and chimera 1.2303 (1006/10/23). Does anybody have similar issues or know what to do about it. Other functionalities of chimera work just fine. Markus

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independent movement
by michel dedeo 09 Mar '07

09 Mar '07

I would like to use Chimera to make a movie in which multiple models or chains move in different directions simultaneously. The movie illustrating myosin thick filament analysis (http://www.cgl.ucsf.edu/chimera/animations/movies/myomovie.mov) is a good example. I am not sure if this post (http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-June/000843.html) on interpolated model motion is relevant, or if the 'movemodel' command imagined there actually exists in some patch that I do not have. If that proves too difficult (I have little programming experience) I would like to be able to hold one model or chain stationary while moving another. I can do this by using the model panel to make one model inactive while entering a movement command to move the active models, but I have not found a way to do this through the command line. Is there a command to activate/inactivate models, or another way to move some models/chains and not others? Thank you for your help. Michel Dedeo Francis Lab Department of Chemistry UC Berkeley

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Stereo using X11 versions
by Eduardo Sanz Garcia 08 Mar '07

08 Mar '07

I have had problems using the stereo capabilites of chimera using stereo glasses. I have two computers: * Mac G5 Quadro PPC + Nvidia FX 4000 with the latest drivers + Chimera X11 version 1.2304 * Fedora Enterprise 2 x Intel Xeon + Nvidia FX 3500 with the latest drivers + Chimera Linux 32-bit version 1.2349 The stereo hardware is correctly installed. I have other applications (X11 pymol) that display stereo nicely in both systems. On the mac, I have been able to display things in stereo but it crashes or displays weird stuff on the screen. On linux, I haven't been able to display things in stereo. Any suggestions? Thank you very much.

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savepos/reset problem with sessions and volumes
by Thomas Goddard 08 Mar '07

08 Mar '07

Hi Christopher, The problem is that Chimera does not preserve the model numbers of volume data sets when it restores a session. Restoring a saved position then moves the wrong models because it remembers the position associated with each model number. There are two Chimera bugs here. First the volume data restored from a session file should use the original model numbers. And secondly, even if the model numbers were to change, the savepos information should be updated to use the new model numbers. These problems exist in all versions of Chimera on all platforms. I'll work on fixing them and send you email if I get it working. I think I can fix the code so that your existing session files will restore correctly using the original model numbers. Tom Christopher Akey wrote: > Tom- > > I am using a build of Chimera from 11/08/2006 for windows. This version > is useful for us because the map to map correlation (fit map) and the > transform as both work nicely. > > However, I tried the savepos/reset within a session today. Set up a new > session that I would not be changing or if so, only by adding additional > files to the end of the listed files. The problem is that when I close > the session and recall it, then the reset commands invariably leave one > or two volumes out of alignment. The problem is that every time I open > the same session, the model list changes order, ie it does not seem to > be completely set in stone. If only one of your aligned images changes > order (actually 2 then), then all your previous commands are for naught, > unless you go ahead and realign them in the current session. Problem is > you don't realize they are misaligned until after you use reset and must > immediately undo move, or you are screwed. Also, you might have a > mixture of brix and mrc files, such that you might not always be able to > recover the right alignment for a file. > > Is this a windows version feature? I have noticed my files not behaving > properly before, but now have pinned it down. > > Do the models and their assoc numbers absolutely remain the same for ALL > MODELS in the linux version or in a newer windows version? > > The savepos/reset is great, you can theoretically recall you previous > figure positions and reshoot them after tweaking a color for a model or > whatever. > > cheers C Akey >

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Re: [Chimera-users] Red-cyan stereo
by Greg Couch 08 Mar '07

08 Mar '07

On March 7, Tom Goddard wrote: > I do not think Chimera produces red-green stereo, only red-cyan. Greg > Couch in our lab would know. I've sent your question to the Chimera > users groups so he can give a more definitive answer. Yes, for red-cyan stereo, chimera puts the left eye in the red channel and the right eye in the blue and green channels. This allows for stereo viewing of color images with red-cyan glasses, but there are many problems, such as red objects not having any stereo cues because they are in only one eye. You will get the best stereo effect with gray-scale images (shades of gray) and if you do use color, avoid saturated colors. You can see the red, green, and blue components of a color with chimera's Color Editor tool. The color name field can be set to any of the color names in the Actions Color menu. Other glasses, red-blue and red-green, will work well with gray-scale images, but will have greater problems with ghosting (ie., part of one eye's image appearing in the other's) in color images. Ghosting will always be present to some degree unless the glasses are perfectly matched to the frequencies of light emitted by the display. So the best advice is to color your data various shades of gray. Hope this helps, Greg Couch UCSF Computer Graphics Lab

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Re: [Chimera-users] copy cmd in nogui script
by Eric Pettersen 08 Mar '07

08 Mar '07

On Mar 8, 2007, at 8:21 AM, Randy Heiland wrote: > Eric, > I just got around to trying this and am told: > “You need to accept the POV-Ray end-user license in GUI mode first” > > (using the 1.2352 snapshot). > Suggestions? > -Randy Hi Randy, You are required to accept the POV-Ray license. However, once you have accepted it, Chimera will remember that and won't keep asking you. So if you start up Chimera normally and save any kind of POV-Ray image and accept the license, you will then be able to run your script in nogui mode on the same machine without the licensing request halting the script. If this is still a problem for the way you want to use the script, let me know. We still intend to make it possible to save non-ray traced images in nogui mode, but prioritizing that would depend on whether POV-Ray images are going to work as a stopgap measure or not. --Eric > From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Sent: Friday, March 02, 2007 8:35 PM > To: Chimera BB > Cc: Randy Heiland > Subject: Re: [Chimera-users] copy cmd in nogui script > > With POVray in the latest snapshot, you can now use the "raytrace" > keyword of the copy command to get a ray-traced image in nogui mode. > > --Eric > > > On Feb 9, 2007, at 8:03 AM, Elaine Meng wrote: > > > Hi Randy, > It is my understanding that the GUI is used to render the image, thus > it is not possible to save images when in nogui mode. (Others, please > correct me if I've gotten this wrong!) > Best, > Elaine > > On Feb 9, 2007, at 7:46 AM, Randy Heiland wrote: > >> What cmd should I invoke in a --nogui script to copy the rendered >> image >> to a file? >> >>> From the interactive viewer cmd line, I can successfully execute >>> 'copy >> file foo.png png'; however, when trying to execute the following: >> >> % chimera --nogui cmd:dostuff >> where 'dostuff' is: >> open 1yc4 >> color byelement #0 >> copy file foo.png png >> >> I get: >> Fetching 1yc4 from web site www.rcsb.org >> Done fetching 1yc4; verifying... >> Opening 1yc4... >> 1 model opened >> Opened 1yc4 containing 1 model, 1890 atoms, and 427 residues >> Rendering high resolution image...Error while processing cmd:dostuff: >> AttributeError: '_chimera.NoGuiViewer' object has no attribute >> 'pilImages' >> (see reply log for Python traceback info) >> Traceback (most recent call last): >> File "/home/heiland/chimera/build/share/__main__.py", line 59, in ? >> value = chimeraInit.init(sys.argv) >> File "CHIMERA/share/chimeraInit.py", line 298, in init >> prefixableType=1) >> File "CHIMERA/share/chimera/__init__.py", line 1217, in open >> File "CHIMERA/share/Midas/ChimeraExtension.py", line 28, in func >> # lswdir = os.path.split(thisdir)[0] >> File "CHIMERA/share/Midas/midas_text.py", line 91, in >> processCommandFile >> File "CHIMERA/share/Midas/midas_text.py", line 60, in makeCommand >> File "CHIMERA/share/Midas/midas_text.py", line 542, in doCopy >> File "<string>", line 1, in ? >> File "CHIMERA/share/Midas/__init__.py", line 795, in copy >> File "CHIMERA/share/chimera/printer.py", line 705, in saveImage >> AttributeError: '_chimera.NoGuiViewer' object has no attribute >> 'pilImages' >> >> >> thanks, Randy >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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View scale and brix output
by Tom Goddard 08 Mar '07

08 Mar '07

Hi Christopher, If I understand your request you want to be able to easily return to a standard view magnification for making figures. There are 3 parameters that determine the apparent size of models seen in the Chimera window: the distance of the models from the eye position, the angular field of view, and the scale parameter which relates the screen pixels to physical units (Angstroms). With orthographic projection only the scale parameter matters. Chimera can use orthographic projection (activated in Camera tab of Side View dialog) but the default is perspective projection where all 3 parameters matter. Assuming you don't change the distance between the eye (i.e. camera) and the models, and you don't change the field of view then setting the scale alone would be sufficient to return to standard magnification settings. In the Side View dialog (menu entry Favorites / Side View) under the Camera tab there is an entry field for the scale factor. It gives the current absolute scale factor and can be changed to whatever value you like. It starts out as 1.0 in a new Chimera session. But if you open a session file it is set to whatever it was in the original session. If you open a session for a figure, then modify it, changing the scale as you go, then want to return to the original session scale factor you could use the command "reset session-start". This not only resets the scale but also the positions and orientations of all the models. Maybe that is not what you want because the new figure is perhaps showing the models from a different direction (e.g. rotated by 90 degrees). So perhaps you need a command like "resetscale session-start". That resetscale command does not exist but I could probably add it if you think it is what you need. Regarding writing BRIX map files, I agree it would be handy if Chimera could output more map formats. I think BRIX format is well enough documented that it could be done (writing files requires better understanding of the format than reading them). That format only saves unsigned 8-bit data values though. So going from float values in MRC to BRIX will lose information. Maybe Chimera would issue a warning about that. Tom Christopher Akey wrote: > Tom- > > A few more issues that have come up for user friendliness. > > 1. It would be useful to have a box where the user can specify the > absolute scale for the session, the first time it is opened, this > could be set at 1.0 for example after loading a ribosome map and the > atomics and putting them to a good size. > > Then the program should keep track of the changes made during the > session using the scale command (I guess you can't track changes made > with the mouse so one generally would avoid this, or even better one > should be able to turn off the mouse scale feature!). > > This way one could always look at the pull down for the current scale > value when you capture a particular view for a figure. > > One could then return to the original scale of 1.0 at the end of > session or write down the current scale value, which could be kept in > the ssesion. So upon reopening the session at a later date, one can > always get back to the correct scale to recapture a panel for a > figure. This is currently a real problem, as far as I can tell. > > 2. We often want to import a brix file with aligned pdbs, since we > dock and look at them in 'O', which is better in some ways for looking > at these maps, but not so good as Chimera for figure making > obviously....then in Chimera we may continue to trim or segment a map, > and then we want to take it back out, presumably as an MRC file, to be > converted into a brix by a conversion program (for us its SPIDER). > Then one can do another cycle of docking in 'O' using the > refined/cleaned up sub map from Chimera. > > While I can think of one way to do this without losing the relative > origins and thus, the map alignments, it is pretty tedious. If one > could write the zoned or volume erased brix volume back out as a new > brix file, with the correct dimensions and origin, relative to the > brix file brought into Chimera, this would allow you to cycle back and > forth using the best of both programs. > > > cheers C Akey >

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RMSD fit of an object to atom
by Navnit Kumar Mishra 08 Mar '07

08 Mar '07

Dear folks; Is there any simple way in chimera to do rmsd fitting of the object to the atom. I would like to measure the rmsd of an density peak with the atom. Could someone give the detail, how can I do it. And one another thing, how can I get rid of the problem with " At least four atoms should be selected", I am interested to do 'match' for two atoms. Thanks a lot, Navnit

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another snapshot
by Eric Pettersen 07 Mar '07

07 Mar '07

We just put out another snapshot (1.2352). It fixes some problems in the previous snapshot, including the scaling in the side-view window not matching the scaling in the main graphics window, and phylogeny support in Multalign Viewer not working. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Chimera to O and back again
by Tom Goddard 07 Mar '07

07 Mar '07

Hi Christopher, Ok, I see, you convert your MRC map to BRIX for working in O but then bring the PDB model that was adjusted in O back into Chimera and realign it with the original MRC. It sounds like the painful part of this process is that the BRIX map does not align with the original MRC map when viewed in Chimera. That is a problem with the SPIDER conversion from MRC to BRIX losing or interpreting differently the origin information. If the BRIX map actually had the correct origin so it aligned perfectly with the MRC map in Chimera then it would save you a bit of trouble. One solution is of course to have Chimera write out the BRIX file so it gets the positioning correct. I'm not sure when I would find time to write that code. Perhaps another solution is to figure out how the SPIDER conversion messes up the origin. That might allow choosing an MRC origin in Chimera such that the SPIDER BRIX map will align with the MRC map. My guess is that Chimera is using the MRC 2000 xorigin, yorigin, zorigin header fields while SPIDER is using the ncstart, nrstart, nsstart header values which Chimera sets to zero when it writes an MRC 2000 format file. If this theory is correct, the BRIX map might align with the MRC map if you change the MRC origin to (0,0,0) using the Chimera volume dialog Features / Origin and Scale panel. You could save this MRC map and work with it to avoid the BRIX/MRC misalignment problem. Tom Christopher Akey wrote: > Tom- > > As to our problem with getting files back into O without degradation of > information. Here is what we found that works. > > You have an original image in mrc format(1.mrc)=> convert to brix (we > use SPIDER) > > Then in O one can dock pdbs & do modeling etc. So now one has a brix > file and pdb modeled in approximately the right area. However, you want > to see if you can improve this difficult modeling. > > So you take the brix file and the pdb into Chimera. > > You write out the brix file as a new mrc file, ie 2.mrc, without any > transformations. > > You then read in the original (1.mrc) and move 2.mrc relative to 1.mrc > using local movements with mouse and then the the map vs map fitting. > > You then transform the fitted pdb file into the original 1.mrc using > "transform as" following the changes to the 2.mrc file. > > You can now do a zone or zone followed by a step of volume erase around > the pdb file using the 1.mrc file, they are in the same relative > orientation now. > > Finally, you write out a zoned/ve map, 1_zone_pdb.mrc, using the 1.mrc > map, so no loss of resolution here. > > Then you can convert 1_zone_pdb.mrc to a brix file and look at in O with > the pdb and it will now be docked in the correct way, ie one won't have > lost the correct origin/alignment of the pdb to the zoned map. > > ------ > > At this point in O, one can adjust the modeled pdb in the zoned density, > then bring the brix file and new modeled pdb files back into Chimera to > make a figure with a better fit of the modeled pdb file. > > This is obviously only needed when you have two structures interacting > and need to segment them vary carefully, to try and improve the local > fit of a loop or whatever. > > Did this make sense? > > It is a way to work in Chimera then transfer back > into O to visualize and work there and even to cycle between them. > > > cheers C Akey

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