- Chimera-users - RBVI Mailing Lists

error parsing ATOM record when coordinate long-ish
by Miguel Ortiz-Lombardia 02 Apr '07

02 Apr '07

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, I can't read a particular atom line that looks like: ATOM 4 CA GLY A 4 -32.686-186.362 -1.715 1.00 20.00 C I presume that the reason is that the y-coordinate forms a continuous string with the x-coordinate. However, this line complies with the PDB format; I quote from the RCBS site: 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms I realize that this may be seldom a problem, but I think it should be tackled. In my case, this is a dummy atom to represent a dipole moment vector with quite a big magnitude. I have the same problem in the last and the previous snapshot versions of chimera (both in linux and MacOSX) Thank you in advance, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFGD2QuF6oOrDvhbQIRApSSAJ94MwNKKsPowzYE/k61g9Yen1PArwCfSnWJ gUXmMlHVsrRuLscR3IWg/tQ= =6/U1 -----END PGP SIGNATURE-----

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error parsing ATOM record when coordinate long-ish (II)
by Miguel Ortiz-Lombardia 01 Apr '07

01 Apr '07

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi again, I forgot to mention that I solved my particular problem by using a bild object to depict the vector. Just thought that the parsing of the ATOM record should be fixed. Cheers, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFGD2u7F6oOrDvhbQIRAvWJAJ9UiNDLaAv9yDbf6HPoNyhHVaGAmwCfd1SF ZHM9NIY3QX5mjFVqNdvvTQk= =Gbf0 -----END PGP SIGNATURE-----

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can 2D label font be bold?
by EJ Pone 27 Mar '07

27 Mar '07

Hi, I was wondering if there's a way to make the font of 2D labels bold. I can change the font of labels associated with atoms/residues etc thru Favorites > Preferences > Background > Label font > Bold, but I can't figure out how to do this for 2D labels. The reason I am interested is that the bold font looks really appealing in labels when I make movies, but the regular font for 2D labels looks a little bit weak. Thank you for any suggestions. EJ UC Irvine

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Re: [Chimera-users] per-model clipping plane
by Thomas Goddard 26 Mar '07

26 Mar '07

Hi Jean-Francois, There is not yet a command specifically to move per-model clip planes. But you can do it using the "savepos" and "reset" commands. These save and restore the positions of all models and the per-model clip plane positions (Chimera 1.2352 and newer). For example, you can save an initial position with command savepos p1 then move a per-model clip plane with the mouse to a new position and save that savepos p2 then to smoothly go from position p1 to p2 over 100 frames use reset p1 reset p2 100 The named positions are saved in Chimera session files. Saving of per-model clip positions when you use savepos was added very recently (March 1, 2007) so you need Chimera snapshot version 1.2352 or newer. Formerly just the model orientations were remembered. Tom jean-francois menetret wrote: > > Hi Thomas, > > is it possible to move the per-model clipping plane using a > movie-related command ? > > Jean-Francois > >

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need help to run chimera 1.2304-linux.exe
by 김소연 26 Mar '07

26 Mar '07

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saving image as stereo pair
by Boaz Shaanan 25 Mar '07

25 Mar '07

Hi, It seems to me as if the stereo pair produced when I select 'stereo pair' in save image is crossed-eye stereo (not wall-eye), or is my brain fooling me ? I certainly see a left-handed alpha helix, residues in the front going to the back and D-amino acids when I use my stereoviewer. Please advise. 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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Counting atoms within density map contour
by Tom Goddard 23 Mar '07

23 Mar '07

Hi Gary, You asked yesterday whether it is possible to count the atoms lying outside the contour surface of a EM map after fitting. This can be done although it currently requires a few steps. Here's how. 1) fit the atomic model into the map as desired. 2) Use menu entry Tools / Volume Data / Values at Atom Positions, choose the molecule and map and press the Histogram button. This shows a histogram of the map values interpolated at the atom positions. 3) Press the "Select" tab on the Render / Select by Attribute dialog and choose Attribute "value_mymap.xxx", move the rightmost green bar on the histogram to match the contour level, then press the Apply button. This procedure selects the atoms at lower density levels than the map contour level and you can see the number of atoms selected in the lower right corner of the main graphics window. You can press the up arrow key a few times to select all atoms in the molecule to see the total number of atoms. I show a picture below fitting 1i84.pdb into myosin.map where 2727 of 16070 atoms lie outside the contour surface. I colored the selected atoms outside the contour blue in the picture. Tom

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osx headers
by Randy Heiland 23 Mar '07

23 Mar '07

Out of curiosity, what is different in the ppc and intel headers for 1.2349? I see that both are available on the Source download page. -Randy

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installing chimera over an older chimera install?
by Sabuj Pattanayek 23 Mar '07

23 Mar '07

Hi, On *nix is it safe to install a newer version of chimera over a previous installation? Will this break something in the newer installation? The reason why I ask is the trouble of maintaining externally installed plugins. We could make a wrapper for the .exe unzipsfx install and re-build symlinks to an external directory of chimera plugins in the share directory, but this seems like too much trouble especially if just installing over an old installation should just "work". Thanks, Sabuj

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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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Re: [Chimera-users] View scale and brix output
by Eric Pettersen 07 Mar '07

07 Mar '07

Just to clarify some of the things that Elaine was unsure of: if a model gets closed that was involved in saved positions then it will simply be ignored when the position is restored. If some new model gets the same ID and sub-ID # as the closed model then that model will be positioned as if it were the closed model (except for per-model clip planes). --Eric On Mar 7, 2007, at 12:24 PM, Elaine Meng wrote: > Hi Christopher, > As long as you save the session after using savepos the positions > should be there. However, as you suspected the model numbers are > important - the individual transformations for the models are restored > based on those model numbers. I think it will restore the positions > of whichever models are there, despite complaining that some are > missing (it's been a while, I'd have to try it to make sure). If you > closed model 0 and opened a new model 0 it might try to put it in the > position the old model 0 was in. Also not sure about that one. When > I use saved positions for my own work, I don't delete/add models > between saving and restoring the positions. > > I can't really envision how positions could be saved without using the > model numbers. The only other thing I can think of is data file name, > but frequently one will have the same data file opened as more than > one model at a time, with different transformations. > ----- > 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 7, 2007, at 12:15 PM, Christopher Akey wrote: > > Elaine - > > yeah,that does seem to work nicely within a session, lets see what > happens when I close and reopen it. However, is the savepos option > sensitive to things like deleting one object from the session before > closing, then opening and adding a new object (now the numbering of > the objects may vary and this seems to screw up matrices that are > saved cause they depend on the numbers). I would hope that savepos > doesn't depend on numbered objects? > > cwa > > > Meng wrote: >> Hi Christopher, >> Tom did mention "reset," but I thought I'd expand on that topic a >> bit. You can actually save multiple named positions, which will >> then be included in a single saved session. When I make a set of >> figures that differ in view and scale but with basically the same >> display/coloring setup, I use the "savepos" command to save the >> position for each figure, and then save the session. It doesn't >> matter what position everything is in when you save the session, >> because you will still be able to get back to any of those saved >> positions with "reset." >> The saved positions include scale. If you really only want to >> restore scale, currently you could note the value shown in the >> Camera tool (as mentioned by Tom), and later type that into the >> Camera tool to restore it. >> more about savepos and reset: >> http://www.cgl.ucsf.edu/chimera/1.2304/docs/UsersGuide/midas/ >> savepos.html >> http://www.cgl.ucsf.edu/chimera/1.2304/docs/UsersGuide/midas/ >> reset.html >> 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 >> 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 >>> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -- > cheers C Akey > > ------------------------------------------------------------------ > STRUCTURAL ELECTRON MICROSCOPY & CRYSTALLOGRAPHY GROUP > ------------------------------------------------------------------ > Christopher W. Akey, Professor > Physiology & Biophysics > Boston Univ. School of Medicine > 700 Albany St. > Boston, Mass. 02118-2526 > > off: 617 638 4051 lab: 617 638 4088 > fax: 617 638 4041 > cakey(a)bu.edu > http://biophysics.bumc.bu.edu/faculty/akey/index.html > ------------------------------------------------------------------ >

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Re: [Chimera-users] Red-cyan stereo
by Tom Goddard 07 Mar '07

07 Mar '07

Hi Jean-Francois, 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. Tom jean-francois menetret wrote: > > Hi Thomas, > > I have tried the red-cyan stereo option of Chimera with red-green glasses > (I couldn't find red-cyan glasses). One gets the stereo effect but > there is a > shadow from the cyan image that the red filter doesn't stop completely. > Is it possible to change the cyan to green ? > > Jean-Francois

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Re: [Chimera-users] md movie amber issue
by Elaine Meng 05 Mar '07

05 Mar '07

Hi Tom, Recording a movie uses the screen resolution. In contrast, image saving uses "supersampling": a bigger image is saved initially and then sampled back down to the requested size, and that gets rid of jagged edges. Currently, movie recording cannot save the image frames with supersampling, but we plan to add that in the future. If you are recording a trajectory in MD Movie, use the "recording" feature in MD Movie. There is no advantage to using Movie Recorder (under Utilities) or the command "movie" because they use exactly the same underlying mechanism to save frames and assemble them into a movie, and are subject to identical resolution issues. All the same flags that can be used with the "movie" command can be entered in the recording dialog called from MD Movie. The difference is (as you noted) the Movie Recorder is not synchronized well with trajectory playback. See http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ movie.html#recording and the "encode" options in: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html In neither case would you have to assemble the individual frames yourself (unless you wanted to for some reason) - on Movie Recorder, clicking the "Make movie" button encodes the saved frames into a movie file. Settings that affect the final movie appearance are Chimera window size (adjust this before saving image frames) and the encoding options mentioned above. 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 4, 2007, at 4:20 AM, Thomas Caulfield wrote: > Hi again Elaine, > > (I) > So I have a MD movie trajectory working (NAMD style, not AMBER), but > my question now goes to rendering a movie. I noticed that under the > MD trajectory window (which plays the frames), that the net resolution > afterward is pretty low (whether I choose MPEG-1/2/4 or > quicktime.mov). But when I do renderings of images the quality is > amazing. > (II) > I also went to Utilities under tools and movie recording, where it > seems some preferences are listed (like resolution etc.), but when I > hit record under that option the trajectory doesn't play, so It starts > taking high-resolution screenshots into a folder with the name > qui*blah-1,2,3,4,... and so on. If this were to play the trajectory > that would be fine, because I could use graphic converter to make a > movie of that. When I tried to do it manually and the make the movie, > it was better resolution, but jerky skipping tons of frames at a time. > > Is there an easier way to do it in (I) and set some preference to the > desired resolution (it looked all bitmappy and fuzzy by the end), > rather than trying to take 1000+screeshots from method (II)? > > Thanks again. > > -Tom > > PS I will try getting this to that other email you gave before thanks. > > On Mar 3, 2007, at 1:26 PM, Elaine Meng wrote: > >> Hi Tom, >> For some reason the mail came to me and not Eric! It may be because >> his address was typed with a one instead of an ell (should be cgl not >> cg1) - but no harm, I've forwarded it to him. He will have to address >> the first question, but I'll tackle the other. >> >> In single-PDB input, the frames should be indicated with MODEL and >> ENDMDL records. For an example, see any NMR structure in the PDB >> that has more than one set of coordinates (1plx is a nice small >> example). >> Best, >> 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 3, 2007, at 1:06 AM, Thomas Caulfield wrote: >> >>> Hi Eric, >>> >>> I wanted to know about using Amber prmtop with Chimera movie md >>> traj. I used it and my initlal frame looks fine, but then it starts >>> bouncing out of camera and back, and my final molecule looks a mess. >>> But in VMD it looks just fine. I'd rather use Chimera for >>> rendering since everything looks so nice in it, however I don't know >>> why it is doing this. >>> >>> I also tried using a series of PDBs instead (to circumvent this >>> issue), but I cannot load it as a single PDB (with multiple frames >>> in it), since the program complains there is only 1 structure in the >>> file. I removed all END and added numbers between the files to try >>> and get it to realize there were frames. >>> >>> What can I do to fix this? >>> >>> Thanks a bunch! >>> >>> -Tom >>> >>> _____________________________ >>> Tom Caulfield, Ph.D. Candidate >>> School of Chemistry & Biochemistry >>> Cherry Emerson Bldg., RM 329 >>> Georgia Institute >>> of Technology >>> Atlanta, GA 30332-0400 >>> Harvey Laboratory: >>> http://rumour.biology.gatech.edu >>> _____________________________ >>> >>> >>> >> > >

2 1

copy cmd in nogui script
by Randy Heiland 02 Mar '07

02 Mar '07

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

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snapshot release source
by Randy Heiland 02 Mar '07

02 Mar '07

Would it be possible for the dev team to post the source headers for the 1.234*/numpy snapshot release? -Randy

2 1

Virus map density versus radius
by Tom Goddard 02 Mar '07

02 Mar '07

Hi Padma, I added a Chimera keyboard shortcut "rd" that prints out average map density versus radius. https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/radialden… This zip file contains a directory RadialDensity that you put in chimera/share. You enable keyboard shortcuts with Tools / General Controls / Accelerators On, open your VIPER map and type shortcut "rd". A table of radius and average density values is displayed in the Chimera reply log. You can copy and paste it to a plotting program. I've attached an example image for em_1sva. I used the following plotting program on the Mac. http://www.apple.com/downloads/macosx/math_science/plot.html The calculation is very slow because it is done in Python. For em_1sva (size 72^3) it took 12 seconds on my intel Mac and for em_1011 (size 256^3) it took 10 minutes. It could be 100 to 1000 times faster in C++ but that would require more code. I tested with Chimera 1.2343. I will be at the Biophysical Society meeting Sunday through Tuesday and probably not answering email. Tom Padmaja Natarajan wrote: > Tom, > > I was also wondering if it is possible to get "max. radius" value for > every entry by > radially averaging the density values for radii going in steps of the > pixel size of that map. > Then we do not have to give the radius value in the input text file > and also will be able to produce a text > file with "radius vs. average density" for each entry. Just a thought. > > Thanks > Padma >

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Fitting and measuring lengths in volume data
by Tom Goddard 02 Mar '07

02 Mar '07

Hi Mazdak, To fit a PDB model in a map in Chimera you can hand place the model in roughly the right location and then do a computational optimization that maximizes the density at the atom positions. Here are instructions: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmod… Your map grid plane spacing has to be set correctly in Angstroms since the PDB model coordinates are in Angstroms. Adjust the map grid plane spacing using the volume dialog menu entry Features / Origin and Scale and change the Voxel Size entry fields and press the Enter key to use those new values. Voxel size is the same as grid plane spacing. You can measure the length between two markers. Just select the link (ctrl click on it with the left mouse button) and use keyboard shortcut "pl". You first have to turn on keyboard shortcuts using menu entry Tools / General Controls / Accelerators On. Here are more details http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#pathle… For more info on volume data capabilities look at the Guide to Volume Data Display http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html I will look at map merging today if I have time. So far I have been busy all week. Tom Mazdak Radjainia wrote: > Hi Tom, > > There are actually two more tasks where I was hoping that chimera could help > me. > > 1. I would like to fit high resolution data from a coordinate file in a > low-electron density map. Can chimera perform such a docking/fitting? I > tried to do it manually but I couldn't resize the opened pdb file towards my > .mrc electron density map. > > 2. Is it possible to measure the length of a link between two markers? I > tried to use the experimental "distance to surface" feature. But it never > measures the distance between two markers which I hoped it could do. > > I really appreciate that you are already helping me out with map-merging > feature which I hope doesn't cause too much trouble. It's just great to know > if I could do the entire molecular visualization and structure analysis in > chimera? > > Cheers > Mazdak >

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Re: [Chimera-users] yet another chimera question...
by Eric Pettersen 01 Mar '07

01 Mar '07

> On Jan 19, 2007, at 11:13 AM, Elaine Meng wrote: > > > One other thing you might not know is that you can save multiple > > positions in a single session (i.e. you don't have to save a session > > for each position). Positions are named/saved with the command > > "savepos" and reapplied with "reset": > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html > > > > These positions definitely include the global clipping plane > > positions. > > I'm not sure about the per-model clipping plane positions. > > They unfortunately do not contain the per-model clip planes yet. > > --Eric I have just added the saving of per-model clipping settings in positions, so it will be in the next snapshot release. A consequence of this improvement is that you will be able to use the 'reset' command to smoothly interpolate per-model clipping in scripts. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: [Chimera-users] 2d labels in chimera
by Elaine Meng 01 Mar '07

01 Mar '07

Hi Eman, We were able to restore your session and save images that included the labels (nice figure, by the way!). I will send you the resulting images in a separate message. It is now sounding like an issue with your graphics hardware and/or drivers. We would like to get information on your graphics setup - the easiest way is to choose Help... Report a Bug from the Chimera menu, which will fill in that information automatically, and send us a bug report. Since we've been trading mails, you don't need to put a lot of additional information in there, maybe just your e-mail address and something like "2d labels not included in saved image". If it is a graphics driver issue, there is not much we can do, but you may be able to improve performance by updating it. Also, we could add the information to our list of known graphics driver bugs. Thanks and sorry for the difficulties, 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 1, 2007, at 5:50 AM, Eman Ghanem wrote: > Hi Elaine: > I e-mailed you last night and mentioned that the chimera 2d labels > are fine now. After that, I started working on a different file and > the I had the same problem (2dlabels not showing in the image > file). I am not sure where the problem is. I hope this is OK, but > I am attaching the session file including the labels Would you > please try to save is and see you have the same problem? Also, you > asked if I tried different image formats; I tried but the file type > does not make a different. Thank you. > Regards, > > Eman

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2d labels in chimera
by Eman Ghanem 28 Feb '07

28 Feb '07

Hi: I am not able to save an image that contains 2d labels as a Tiff file. Every time I save it, the labels don't show up on the image. I read on your web site that this only happens if I am trying to save an image that is smaller than the original pixels of the chimera window. However, I tried saving it without changing any specifications. Any idea what I can do?? thanks, EG --------------------------------- Don't get soaked. Take a quick peak at the forecast with theYahoo! Search weather shortcut.

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64-bit Linux chimera snapshot available
by Greg Couch 27 Feb '07

27 Feb '07

If you are running a 64-bit version of Linux with an AMD64, Opteron, or Intel Xeon processors, then please try out our new snapshot at <http://www.cgl.ucsf.edu/chimera/download.html>. This platform is now supported and will have future snapshot and production releases. Greg Couch UCSF Computer Graphics Lab

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Re: [Chimera-users] Saving model positions
by Tom Goddard 27 Feb '07

27 Feb '07

Hi Christopher, If you have 10 models open in a Chimera session and you close model number 7, the session should still save correctly. If it doesn't please report it as a bug. Unfortunately restoring the session file uses different model numbers for the density maps (the lowest available numbers). That is a bug that I need to fix. It should use all of the original model numbers even if there are gaps. Even though the model numbers will change, the orientations of all the models 1-6 and 8-10 will all be correct in the restored session. I sent your earlier email to our Chimera users mailing list. That is why your reply to me went to that mailing list. I like to post the questions to the mailing list so others can benefit from the answer and I remove any confidential information (email, phone, signature line, research details). Let me know if you want to keep your questions off of the Chimera mailing list. Here's the message where I posted your original question and my reply. http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001366.html Tom Christopher Akey wrote: > > Thomas - > > This went via reply to some kinda list, sorry. > > I will try some of these approaches. However, there is a question. If > you have 10 objects in a session, and decide to delete number 7, then > sometimes you cannot get the session to save properly with a missing > number. > > In theory, if one could get the session to save, then a matrix for the > first 6 objects would still work? > > > cheers C Akey

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New chimera development snapshot available
by Greg Couch 26 Feb '07

26 Feb '07

See <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html> for details (this will be accurate for the next few days, after that read the release notes that are bundled into the chimera snapshot). The snapshot uses NumPy instead of Numeric python, so some third-party extensions may break (eg., parts of EMAN). Other highlights include intial support for PDB 3.0 (remediated PDB) format and built-in POV-Ray raytraced image support. Enjoy, Greg Couch UCSF Computer Graphics Lab

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Saving model positions
by Thomas Goddard 26 Feb '07

26 Feb '07

Hi Christopher, The problem you have with the Chimera matrixget and matrixset commands is that the matrix file lists the model number (0.0, 1.0, 2.0, ...) with each matrix. For example, Model 0.0 -0.0635922 -0.740419 0.66913 247.807 -0.979146 -0.0833402 -0.185275 540.192 0.192946 -0.666958 -0.719679 472.752 Model 1.0 0.233245 -0.923975 -0.303095 418.621 0.970522 0.201738 0.131868 -125.304 -0.0606967 -0.324918 0.943792 100.98 When you open maps and PDB files in a different order they get different numbers. Chimera assigns the lowest available number (starting at 0) each time you open a data set. Then when you use matrixset <filename> to get your standard orientation it applies the matrices to the wrong models because of the different numbering. The easiest remedy for this is to open your data sets in a fixed order (first large ribosomal map (#0), then small ribosomal map (#1), ...). This can be inconvenient. If you save a single positioning matrix in a file there is no current command to say to apply that matrix to a model that you specify as a command argument (e.g. no command like "matrixset <matrix-file> <model-number>" exists). There are some other approaches to the problem of getting standard orientations. One method is to save your ribosome large and small subunit map positions in a Chimera session. Then if you want to use different maps, open the reference session, then open the new maps and use the "matrixcopy" command http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html to position the new maps to match the reference map positions. Instead of using matrixcopy you could use the equivalent Model Panel dialog "Transform As" button to apply the positioning matrix of one map to a second map. Another command that may be helpful is "savepos <name>". http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html It remembers the positions of all currently opened data sets and gives a name to that set of positions. You can later restore those positions with the command "reset <name>". These named positions are saved in Chimera session files. The trouble is that there is not an immediate way to apply those positioning matrices to different maps or PDB models. But that could be achieved with the matrixcopy command or Model Panel / Transform As button. If this set of capabilities does not let you easily do what you want could you describe an exact scenario (how many maps, how many models, how are they related) and if possible propose a new command that would help you. I think it would be great if density map file formats supported saving multiple named positioning matrices in their header. For example, you might want to save how a piece of a map is positioned in the full source map, and also how a piece of a map fits into different map (e.g. at various locations in a tomogram), and your case of just a standard orientation ("front view", "top view"). I do not believe any of the commonly used density map formats allow this although it may be possible to put that info into header comment fields in some map files. Tom Christopher Akey wrote: > Tom - > > ... > > Chimera is very good, but there are still problems. A new workstation > will help and will be here in a few weeks. > > However, one thing is really annoying. It is important to set a > particular view for your structure, for example a side-by-side frontal > view of the ribosome with regards to the small and large subunits. > > Once you have this in one session it would be useful to be able to > recreate this easily in other sessions. (For logistical reasons, it is > ofter easier to keep a session for each Figure so that they don't get to > crowded.) > > Right now, if you save a matrix (matrixget) and then make a change in > the session, ie delete or add a file, you get unpredictable results, but > usually, the matrix no longer works or it only works for one volume in > the session. This is not good when you have separate vols for the small > and large subunits in proper registration, you get a matrix for the > front view, and then at a later time, only one subunit will be realigned > properly! > > It would be great if you could set a matrix for a particular map as a > benchmark, then when you read that map into any other session, you could > recreate this orientation using the matrix. I don't understand why this > won't work. > > The feature of being able to bring in other maps and align them in > CHimera is great and works very well (its in our older test version that > we are using, and its very useful as we often have 3 or more structures > of the same basic object with minor diffs). > > I hope this makes sense. > > cheers C Akey >

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many days after...another question Re: Select atom by serial number.
by Jean Didier Pie Marechal 26 Feb '07

26 Feb '07

Hi everybody, I'd like to select a series of atoms by their serial number (again!!!) (e.g. from atom number 1 to atom number 10). the sel @/serialNumber=1-10 doesn't seem to be the right syntax. Is it possible to do this kind of selection? If yes, what is the right syntax please. Cheers, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdonyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Elaine Meng <meng(a)cgl.ucsf.edu> Data: Dijous, Gener 11, 2007 8:59 pm Assumpte: Re: [Chimera-users] Select atom by serial number. > > Hi JD, > We also tested Chimera 1.2309 on Windows, and these specifications > > work correctly. Example: > Command: sel @/serialNumber=232 > will select NZ of Lys 27 in chain A of the PDB entry 1zik. The > only > other thing I can think of (besides what was in the previous > message) > is to check if your PDB file is correctly formatted. The > ATOM/HETATM > serial number is supposed to be in columns 7-11 and right-justified. > Best, > Elaine > > On Jan 11, 2007, at 11:39 AM, Elaine Meng wrote: > > > Hi JD, > > You are using the correct specifications - both of your examples > > > should work. I tested both approaches in Chimera 1.2304 on Mac > OSX > > and they worked correctly. We'll have to look into your > specific > > version/platform and get back to you. If you want, you could > send > > me the PDB file you are using so I could test if there is some > > issue specific to that structure. To be clear: the serial > number > > is the number shown in the column after ATOM (or HETATM) in the > PDB > > file, regardless of what order the atoms are really in. That > is, > > if the first ATOM has 2 in that column, its serial number is 2 > and > > not 1. > > Best, > > 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 Jan 11, 2007, at 10:47 AM, Jean-Didier Maréchal wrote: > > > >> Hi Everyone, > >> > >> > >> > >> > >> > >> I am desperately trying to select an atom of my pdb by its > serial > >> number. > >> > >> Looking at the archives, it seems that I should put something > like > >> @/serialNumber=525 > >> > >> I tried “sel #0@/serialNumber=525” in the commandl ine and “@/ > >> serialNumber=525” in the Atom Specifier. None of these > selections > >> worked. Can someone tell me the right way to do this, please ? > >> > >> > >> > >> Cheers > >> > >> JD > >> > >> > >> > >> Current running chimera: version 1 build 2309 > >> > >> OS: windows > >> > >> > >> > >> _______________________________________________ > >> Chimera-users mailing list > >> Chimera-users(a)cgl.ucsf.edu > >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

2 1

Combining 2 electron density maps in 1
by Mazdak Radjainia 23 Feb '07

23 Feb '07

Hi, I would like to open two electron density maps in chimera and save/merge them together in one map. Both maps are activated in the "model panel" but I cannot select/save both at a time using the volume viewer. I appreciate your help! Kind regards Mazdak

3 2

Chimera on 64-bit Windows
by Tom Goddard 21 Feb '07

21 Feb '07

Hi Christopher, I believe the 32-bit Windows Chimera distribution will run on 64-bit versions of Windows, such as Windows XP Pro x64 Edition. But I do not have a machine to try it on. It will certainly run on 32-bit Windows running on a 64-bit processor -- I've tried that with an AMD64 processor. Tom Christopher Akey wrote: > Steve and Tom- > > Will EMAN and Chimera run ok on a 64 bit machine running windows XP, > initially we plan to use it this way, then change over to Linux when > we have time. Or do we just install Linux right away? > > cheers C Akey

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Memory requirements for Chimera
by Tom Goddard 21 Feb '07

21 Feb '07

Hi Christopher, I think it starts making sense to use a 64-bit machine if you are loading data that requires >= 1 Gbyte. In general, 32-bit linux binaries will run on a 64-bit machine. Currently we only provide a 32-bit linux Chimera distribution though we plan on adding 64-bit Linux as a standard Chimera platform in the next 6 months. The 32-bit Chimera runs fine on 64-bit linux. The advantage of a 64-bit version is that it uses memory pointers that are 64 bits so they can address more than 4 Gbytes. On a 32-bit system the operating system and the many libraries that Chimera uses (~50) may occupy a significant portion of the 4 Gbyte address space. Even if you have less than 4 Gbytes of physical memory the operating system can and does use the full 32-bit 4 Gbyte address space and swap data to disk when there is not enough physical memory. But if a program asks for a 512 Mbyte block of memory and there is no available segment of that size in the address space then it will fail. Graphics drivers use the computer's main memory for data that will not fit on the card. Either 256 or 512 Mbytes on the graphics card should give good performance even for large systems. Unless you are using the volume "solid" rendering mode the rendering speed will slow to much less than 1 frame per second before you use up 256 Mbytes. For reference, the machines I currently use for developing Chimera and looking at large volume data sets are: 1) Mac dual G5 desktop with 1.5 Gbyte memory and 128 Mb ATI Radeon 9800 Pro graphics, and 2) MacBook Pro, Intel Core 2 duo, 2 Gbyte memory, 256 Mb ATI X1600 graphics. Thanks for the apoptosome papers -- interesting work. Tom Christopher Akey wrote: > Tom- > ok, I will keep notes on what is not working and send them to you, as > we go through making figures this week. > > Will chimera run fine on a 64 bit Linux box? The other option is 32 > bits, but if I buy a high end workstation it should probably be 64 bit > yes? > > Also, about making Chimera able to handle big sessions: is the rate > limiting factor the RAM or the memory on the Graphics Card. We have a > 512 Mb cache on our current graphics card and still have problems, so > I presume we are RAM limited. > > When buying a new machine, should I invest in a 512 Mb Nvidia card or > is 256 fine, as long as there is enough RAM? > > By the way, I am attaching two pdfs of papers published using Chimera > graphics. > > thanks. > > CWA > > > Tom Goddard wrote: >> Hi Christopher, >> >> I'm not sure what causes crashes in Chimera when you are working >> close to the available memory limit. If a memory allocation fails in >> C++ it should produce an error message in Chimera indicating that >> memory could not be allocated because we catch those exceptions. >> Memory allocations in C (not C++) libraries that Chimera uses are >> likely to cause a crash though. >> >> It would help us to know what Chimera is doing when the crashes >> occur. We may be able to put some safety checks in our C++ where C >> library allocations are known to fail. Do I understand correctly >> that crashes happen while you are saving an image (individual tiles >> being displayed on screen)? Chimera by default makes an image 3 >> times larger then requested to make a smoother image. That can take >> a good bit of memory. Are there other actions that cause crashes? >> >> Tom > >

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An NMR Average Structure
by S W Simon Sham 21 Feb '07

21 Feb '07

Hi, I need to calculate an average structure from an emsembled structures in Chimera. Can we do it it Chimera? If yes, how? Thanks for any helps. Simon ------------------------------------------------------------------------ ----- Simon Sham, Ph.D. NMR Core Facility Comprehensive Cancer Center Univerisity of Alabama 933 South 19th Street CH19 B31 Birmingham, AL 35294 Office: (205) 934-5696 Fax : (205) 934-6475 Email : ssham44(a)uab.edu

2 1

Create surface from markers
by Tom Goddard 20 Feb '07

20 Feb '07

Hi Jeff, Chimera cannot currently create a surface from markers placed with the volume path tracer tool. It would not be so hard to write some Python code to do this. Here is an example of Python code that creates a surface in Chimera: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/surface.html Tom Jeff wrote: > hi Tom, > > is there a way to use a marker file just to render a surface (a > series/group of dots, just needing to be connected by a mesh)? for > instance, to represent a membrane. > > -Jeff

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Saving full map when zoning
by Tom Goddard 20 Feb '07

20 Feb '07

Hi Jean-Francois, You can save a map with the original map size while using volume zone by first pressing the the "Full" button in the Features / Subregion Selection panel of the volume dialog. Then use the File / Save Map As button. You can see what region will be saved by looking at the Features / Region Bounds panel (and you could type in new bounds there and press the Enter key instead of pressing the Full button). The volume zone capability (Features / Zone) normally uses a smaller box of data so that it is faster. Even when part of the surface is hidden by the zoning the whole surface within the box being used is computed and that is sometimes slow. Tom jean-francois menetret wrote: > > Hi Thomas, > > when using the zone option in Chimera, is it possible to have the size > of the saved mrc file (after zoning) be the same as the original file ? > > Best wishes > > Jean-Francois

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Re: [Chimera-users] demo made under Linux has bland atoms in Windows
by Elaine Meng 17 Feb '07

17 Feb '07

On Feb 16, 2007, at 7:55 PM, Kenward Vaughan wrote: > For me, the byatom coloration is there to begin with under Linux. The > ach shows up colored properly, as does the acetylcholinesterase. > Aha!! Problem solved!! I am 99.99% sure the difference is your preferences file. The demo itself does not say to color by element when the structure is opened. However, there is a New Molecules section of the Preferences in which you can say structures should be colored that way when they are opened. Most likely you have this set on your home Linux machine, but not in the Chimera preferences used on the Windows machines. Months ago we discussed the need for some way to indicate that preferences should be bypassed at startup and/or when opening structures. This option would be appropriate for use with demos or scripts to be shared among multiple users each having some arbitrary set of preferences settings. However, this option hasn't been added (nor are we sure how best to implement it)... thanks for the additional motivation to revisit that issue! The demos included with Chimera were made in a directory with a default preferences file. It is likely, however, that some users with nondefault New Molecules preferences have played them back and gotten a result different than intended. > > I've noticed rotation is slow under Windows, but v. nice with Linux > (about 7 seconds total). > It depends on the graphics capabilities of the system. It is slow on our home desktop computer (>5 years old - you can almost hear gears grinding) but fast on my laptop (1-2 years old). Happy demoing and please do contact us with any problems or suggestions, 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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demo made under Linux has bland atoms in Windows
by Kenward Vaughan 16 Feb '07

16 Feb '07

...in a fashion, that is. A demo I plan on using at school (a Windows fortress, it is) displays all atoms as grey--no color (by element). The demo was created on a Linux machine (at my home). :( Any thoughts? Kenward ps. both versions of Chimera are the latest production version (2304). -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

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saving map in different position
by Gabor Papai 16 Feb '07

16 Feb '07

Hi Tom, Is there a way to save a map with only transformation, or obtain the transformation matrix if I do a freehand transformation of an object? We would like to create a composite volume of several spheres. It would be the best to write a single map of several differently positioned spheres but I could also apply the transformation in IMAGIC if I would know the matrix. Thanks for helping! Regards, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-90244796 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

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Re: [Chimera-users] making movies with MorphMap, exporting povray scenes, FitMapInMap
by Gatsogiannis, Christos 15 Feb '07

15 Feb '07

Hello Greg and Tom, povray: the assumed gamma-change was indeed the problem. Thank you very much! I´m waitin for the next snapshot release MorphMap: the updated version works correctly! Thanks! Do you maybe plan in the future on offering the possibility to save a density map also in different formats than mrc (situs, imagic .. etc) ? That would be very useful... Thanks again, Christos

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cavity cropped view
by Randy Heiland 15 Feb '07

15 Feb '07

What options exist in Chimera for letting me show only that portion of a protein that is "near" another smaller molecule? Specifically, I have a ligand in a cavity of a large protein and would like to eliminate the "clutter" of the protein away from the cavity of interest. Thanks, Randy

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making movies with MorphMap, exporting povray scenes, FitMapInMap
by Gatsogiannis, Christos 14 Feb '07

14 Feb '07

Dear Chimera users and developers, recently I used the new morph map tool and it worked very nice in my case. I encountered a problem while exporting the animation in any movie-format within Morphmap, I just get empty or very small files, which cannot be displayed in any media-player. I decided then to use the chimera-movie recorder utility to record the morphing animation and this worked fine (I´ve tested this with mpeg-2 format). At the moment I´m using the chimera-version 1.2309 in a SUSE LINUX 9.2 environment. Is this a version problem or a bug? Furthermore, I´ve exported some scenes in the povray format and I´ve noticed that the final images are of lower quality in comparison with images made some months ago with older chimera versions. I haven´t changed the povray-version, the rendering settings and the settings for the visualisation of my data in chimera (brightness etc...). The colors are too pale, I could send you some example-images if needed. I´ve tried also the Fit Map in Map tool recently and it worked perfectly (you sent this tool to a group-colleague some months ago). I´m wondering why you didn´t put this tool on the experimental site yet....and one more last question...after using Fit Map in Map, is there any possibility to save the "fitted" map with it´s new orientation? Thanks, Christos Christos Gatsogiannis Institute of Zoology Johannes Gutenberg University 55099 Mainz, Germany Tel: +49(0)6131-39-23091 email: gatsogia(a)uni-mainz.de

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Request for Chimera on CD
by Tom Goddard 13 Feb '07

13 Feb '07

Hi Zia, Our Chimera software can be downloaded from the web http://www.cgl.ucsf.edu/chimera/download.html We have never distributed it by CD. Perhaps we can do it. Our program needs about 512 Mbytes of computer memory. What operating system do you need it for? Windows? Linux? Mac OS X? Because almost all molecular structure and sequence data used in research is obtained from the web I suspect our software will be of limited use to you without internet access. Tom zia muhammad wrote: > Respected Dear Dr. > > I am teaching Bioinformatics at International Islamic University > Islamabad, Pakistan. I am teaching molecula Docking and Protein > Structure prediction, CHIMERA or HMMs methodology. I hvae done all > theoratical work but could not perform any practical due to lack of > softwares. I will thankful to you if you kindly provide me some basic > softwares in this respect. After basic knowledge and establishing > proper labs we will purchase relatd softwares but on initial basis we > need your help. I also could not download different softwares so can > you kindly send me on CD. > Your kind attention will be highly acknowledged. > > Please reply. > > Regards > > Zia > > > ******************************** > *Muhammad Zia* > *Room # 7, Hostel # 2* > *Quaid-i-Azam University,* > *Islamabad. Pakistan* > *45320* > *********************************ue

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display two volumes alternatively
by Montserrat Samso 13 Feb '07

13 Feb '07

Hi, I am trying to compare two cryoEM density maps of the same protein, the only difference between them is a conformational change. Is there a way to switch directly from one volume to the other without having to display both of them together in between? Thanks, Montserrat ------------------------------------------------------- Montserrat Samso, Ph.D. Assistant Professor Department of Anesthesia Research Brigham and Women's Hospital Harvard Medical School 75 Francis St. Boston, MA 02115 Tel: 617 7328107 Fax: 617 7326927 E-mail: msamso(a)zeus.bwh.harvard.edu -------------------------------------------------------- CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s). The information contained in this message may be private and confidential, and may also be subject to the work product doctrine. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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programmatic representation
by Randy Heiland 12 Feb '07

12 Feb '07

I'd like to be able to set the representation (wire, stick, bs, cpk) of a model programmatically, in this case, from a plugin. I was trying the following, but the newly displayed model would always be displayed in wire: self.model = ReadSDF.readSDF(tmpfile.name) chimera.openModels.add(self.model) #Midas.represent('stick', self.model) Midas.represent('cpk', self.model) Suggestions? thanks, Randy

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Re: [Chimera-users] opacity for stick representation in chimera
by Elaine Meng 12 Feb '07

12 Feb '07

Hi Jerome, First make a transparent color and then use it on the atoms/bonds - there are a handful of routes. You can make the transparent color using the Color Editor (under Tools... Utilities; click the Opacity to get a slider for that, then adjust the red/green/blue/opacity sliders as desired). This color can be used on atoms/bonds, ribbons, whatever (depending on the current target setting under Actions.. Color) by choosing "Actions... Color... from editor" or it can be used in coloring commands using the color name "fromeditor" Color Editor description: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortool.html Alternatively, you can make the transparent color with the command "colordef" and give it whatever name you want. The new color name can then be used in coloring commands. Color definitions are saved in sessions. Or, if you don't want to save sessions, just make a command file with all of your favorite color definitions and read it in whenever you want those colors defined. "colordef" man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html I hope this makes sense - feel free to write back if it doesn't! Best, E ----- 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 Feb 11, 2007, at 5:14 PM, Jerome Nilmeier wrote: > Hi Elaine: > > I was wondering: can you adjust the opacity of the stick > representation in chimera? > > best, J

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xforms, cpk scale
by Randy Heiland 08 Feb '07

08 Feb '07

Is there a command to scale sphere of a CPK rep? Is there a command to save the current viewing transformation to a file and then read it back/apply it at a later time? Thanks, Randy

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Drawing Artifacts
by Albion Baucom 08 Feb '07

08 Feb '07

Using the latest stable current production release of Chimera, 1.2304, I have begun to experience some drawing problems that I never had in previous versions. Specifically I frequently get a thin wireframe rendering of my protein structure when I draw the structure as a ribbon with a volume open at the same time. This wire frame persists even when I turn the display of the molecule off in the model panel, and it also does not rotate or translate if the protein is selected as the only active object. In effect it leaves behind a ghost image. Curiously this representation alternates from a light gray/white color to black when I open dialog boxes. The artifact toggles on and off with the volume in some instances. My processing and graphics hardware have not changed recently, nor has operating system (Linux). I do not experience this behavior with my last version of Chimera, 1.2199; it never renders this artifact. I have a nVidia Geforce 6800GT graphics card with the nVidia Linux drivers 1.0-9746. My X11 server is version 6.8.2. Here is a screen image of this phenomenon http://msg.ucsf.edu:8100/~baucom/images/chimera_image.jpg I have rotate the model slightly to show that the thin wireframe stays behind. It is not a separate object in the model panel. Thanks Albion

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Morph Map
by Tom Goddard 07 Feb '07

07 Feb '07

I've added a Chimera extension called Morph Map http://www.cgl.ucsf.edu/chimera/experimental/morph_map/morphmap.html to the experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html It interpolates between two volume data sets and makes animations. The original version of this tool was written by Wei Zhang in Pawel Penczek's lab. Tom

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Re: [Chimera-users] Map Orientation for Symmetry Plug-in
by Tom Goddard 07 Feb '07

07 Feb '07

Hi Albion, Ok, I made the "fit map in map" tool print out a point on the rotation axis. The new code for use with Chimera 1.2318 is here: https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/fitmap231… The zip file contains a directory FitMap that you put in your Chimera distribution under chimera/share or on Mac Chimera.app/Contents/Resources/share For more installation details see http://www.cgl.ucsf.edu/chimera/experimental/install.html This FitMap directory replaces your existing one. After restarting Chimera you can fit a helically symmetric map in a rotated copy of itself then get the axis point (shown in Favorites / Reply Log) and adjust the map origin (volume dialog Features / Origin and Scale) to put the axis point at (0,0,0). I described this in more detail in my previous message: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001313.html The output of the axis point will be included in the next Chimera snapshot due out in one to three weeks. The matrix you sent me had no rotation, just a translation by 52 along z. You will need to rotate the map copy before fitting to get a meaningful rotation axis point. In fact I suspect the accuracy will be increased for rotations near 180 degrees rather than small rotations (e.g. 30 degrees). Tom Albion Baucom wrote: > Thanks Tom. > > OK, here is my rotation matrix after following your instructions > > 0.99944468 -0.03326699 0.00190528 -0.09024247 > 0.03326443 0.99944566 0.00136109 0.10539160 > -0.00194951 -0.00129696 0.99999726 52.82194789 > > Sorry, I forgot how to compute the rotation axis vector from this > matrix ... its been awhile since I had to do that manually ... its > pretty simple if I remember right. > > Any code to automate this would be greatly appreciated. > > Thanks again! > > Albion

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colorzone tool
by Jeff 06 Feb '07

06 Feb '07

would it be possible to allow 'color zone' to go past 30 A radius? -Jeff

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Hiding part of a marker set
by Tom Goddard 06 Feb '07

06 Feb '07

Hi Jeff, You can hide part of a marker set by selecting the markers you want to show (maybe using the select connected shortcut "sc" as described earlier) then use invert selection (main window menu Select / Invert, or shortcut "is"), then use path tracer menu entry Actions / Hide markers (or shortcut "ha" for hide atoms). Tom Jeff wrote: > I don't suppose there's a way to hide only a portion of a marker set > (just keep one filament visible out of 10, for instance) > > -Jeff

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Mac laptop benchmark
by Tom Goddard 06 Feb '07

06 Feb '07

Hi Jeff, I ran the Chimera benchmark tool on my new MacBook Pro and got scores: surface 543 mesh 545 contour 183 solid 256 recolor 132 But running hand tests I see the real surface/mesh scores should be 380. It appears the benchmark no longer is reporting correct scores either because a graphics driver optimization is speeding things up because the test image is not actually displayed, or Chimera code has changed (perhaps no longer guaranteeing the OpenGL buffers are swapped). Probably other scores on the Chimera benchmark web page are likewise inaccurate. This will have to be investigated. At any rate, actual surface rendering is about 65% faster than my Dell Precision M50. A test on a GeForce Go 7400 (aka Quadro NVS 120M) in a new Dell Lattitude D820 also gave erroneous scores, but hand testing gave surface rendering score 420 and horrible mesh (110) and solid (<20) numbers. Tom Jeff wrote: > could you run the benchmark on your mac? (I have run it on my > workstation, but forgot the scores; will do again and compare) > > -jeff

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NumPy in Chimera
by Tom Goddard 06 Feb '07

06 Feb '07

Hi Chimera Extension Writers, If you have written Chimera extensions that use Numeric Python you will need to convert them to instead use NumPy to work with future versions of Chimera. NumPy provides almost all the same routines as Numeric but some function and module names have changed. We are switching Chimera over from Numeric Python to NumPy and will have a Chimera snapshot out in one to three weeks that uses NumPy. We envision having a Chimera production release that uses NumPy in perhaps 3 months. The change was necessary because Numeric is no longer maintained. Numeric will no longer be included with Chimera because dynamic library name space collisions with NumPy occur on the Mac because of certain Chimera compilation options. The conversion of Chimera code was not much trouble, but we had to also convert third party packages that are included with Chimera (PyOpenGL, MMTK, Scientific (for netcdf file reading), MSMS molecular surfaces) and that took some work. Thanks for your patience. Tom

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Re: [Chimera-users] question about mac laptops / workstations and chimera stability
by Tom Goddard 06 Feb '07

06 Feb '07

Hi Jeff, I just got my MacBook Pro with 2 Gb memory and 160 Gb hard-drive yesterday. It's been working well with Chimera volume display, surface and solid. Performance is roughly a factor of two better than my 4 year old Dell Precision M50 with Quadro 4 GoGL 500 graphics (a very heavy machine, ~10lb). I just took a look at a 2k by 2k by 76 tomogram and performance was as expected. 2 Gb memory is adequate for my uses. I went for the 160 Gb harddrive instead of the 120 Gb since volume data and video can take some space. The 200 Gb option was a 4200 rpm drive which I suspect would be slower than the smaller 5200 rpm models so I avoided it. If you'd like to try my laptop before you order you are welcome to come over to my house in SF. Tom Jeff wrote: > Tom, > > is the base 2 GB memory sufficient, and do you have any reservations > regarding transfer speed from the harddrive? > > I am going to place an order, wanted to check with you first about > those 2 things before going ahead. > > (I figure, if you are developing on it, this is not a bad idea.) > > -Jeff

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Map Orientation for Symmetry Plug-in
by Albion Baucom 05 Feb '07

05 Feb '07

I am using the Symmetric Molecule Copies plug-in with Chimera. I am wondering if there is a preferred way to orient an EM volume so that it is centered around the z-axis at the origin. From my experience with this plug-in, symmetry related molecules are generated around z-axis at the origin of the viewing area. I am finding that my maps tend to be close, but not exactly oriented around the z-axis for a helical volume. Molecules fit into a portion of the map then tend to have slightly askew symmetry mates relative to the volume (presumably because the z-axis of the map is not exactly oriented along the origin of the symmetry z-axis). After playing around with various map tools (MAPMAN, Priism), I am still not satisfied with my orientation protocol and wonder if anyone can suggest a tried and true method for this. Thanks Albion

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Re: [Chimera-users] volume/3586 problem zoning out volume
by Thomas Goddard 05 Feb '07

05 Feb '07

Hi Jeff, To check the memory limits set by a bash shell use shell command "ulimit -a". For a csh use "limit". Here's an example on my Mac (no memory limit). Tom $ ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) 6144 file size (blocks, -f) unlimited max locked memory (kbytes, -l) unlimited max memory size (kbytes, -m) unlimited open files (-n) 256 pipe size (512 bytes, -p) 1 stack size (kbytes, -s) 8192 cpu time (seconds, -t) unlimited max user processes (-u) 100 virtual memory (kbytes, -v) unlimited Jeff wrote: > I had forgotten about 4-byte floats versus 2-byte integers, > > you are right in that this is most likely a machine limitation, I was > surprised to get a fault and error about an allocation call. is there a > specific environment variable I should check to see if the shell is > limiting chimera's memory requests, I will change that if possible (?). > > -Jeff >

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rotation by a set angle
by Eva Vanamee 05 Feb '07

05 Feb '07

Hi, I am trying to make a figure of my EM fit at different orientations. Is it possible to rotate the molecule/map by a certain angle so I know exactly the rotation between views? Thanks in advance, - Eva

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Re: [Chimera-users] not able to 'transfer markers'
by Thomas Goddard 05 Feb '07

05 Feb '07

Hi Jeff, Menu entry "Actions / Transfer selected markers to current set" in the path tracer dialog moves the markers to the marker set chosen on the first line of the path tracer dialog. That should be the same as the one chosen in the marker set scrolling list (Features / Marker set list) unless that list has multiple sets selected. The error message "Markers in one set cannot link to markers in a different set" means you tried to transfer some markers to the current set but they were connected by at least one link to markers in another set. That is not supported. There is a command, keyboard shortcut "sc" that extends the current selection to all markers connected to currently selected ones. You'll need to turn on keyboard shortcuts with main window menu entry Tools / General Controls / Accelerators On. You can have them turned on by default every time you start Chimera using the Preferences dialog (menu Favorites / Preferences) category Tools and clicking the check button in the autostart column next to "Accelerators On". One possible confusion about hiding/showing markers is that if you have any markers selected then the Actions / Show & Hide menu entries act on those selected ones no matter what marker set they belong to. If there are no markers selected then those same menu entries act on all markers in the current marker set, that is the one chosen at the top of the path tracer dialog. The marker set scrolled list is used for closing multiple marker sets and for saving multiple marker sets. This may have been the problem when you could not close a marker set. It closed the one selected in the scrolled list which was different from the "current marker set" shown at the top of the path tracer dialog. When you change the current marker set menu it unfortunately does not clear the selected marker sets in the scrolled list. That is a bug. Let me know if you can reproduce the problem hiding/showing markers. Tom Jeff wrote: > hi Tom, > > using build 2318, if I select a series of markers, and then click > 'actions -> transfer selected markers to current set', it gives the > error 'Markers not transfered. Markers in one set cannot link to markers > in a different set.' when I did this, I assumed that the 'current set' > meant the one selected in the 'marker sets' dialog box in the volume > path tracer. > > is there a way for me to get around this? I had traced out a series of > actin filaments in one set, and for practical reasons want to be able to > show/hide each marker path that corresponds to a filament; the only way > I could think of doing this was to have each filament be a separate > marker file, unless there is a command that allows me to select a single > marker and then just 'display markers connected to selected marker' > (preferred, actually), as opposed to using the up-arrow, which selects > the entire set. > > after performing the 'transfer markers' request, I was no longer able to > show/unshow the marker sets. Also, when I closed a marker set, it was > still displayed. I shut down the session and recreated it from scratch. > I'll let you know if this show/unshow/close marker file issue occurs > again and under what circumstances; it would be hard for me to claim > that it was correlated to the 'transfer markers' command, I just know > that after that point in the session I could no longer show/unshow/close > the markers. > > thanks, > > -Jeff >

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PDB file format for movie
by Mingfeng Yang 05 Feb '07

05 Feb '07

Dear Chimera users and developers, I'd like to use chimera to view the motions of a protein. If all the snapshots are to be saved in a single PDB file, what's the correct format for them? I tried the following, but chimera complained that a single structure is included only. Thanks, Mingfeng ------------------ MODEL 1 ATOM 1 N ALA 1 -4.564 -7.956 -6.531 1.00 0.00 N ATOM 2 CA ALA 1 -5.237 -8.746 -5.532 1.00 0.00 C ATOM 3 C ALA 1 -4.360 -9.172 -4.378 1.00 0.00 C ... ATOM 81 HN ALA 10 0.195 11.398 3.736 1.00 0.00 H END MODEL 2 ATOM 1 N ALA 1 -5.031 -8.234 -5.174 1.00 0.00 N .... END

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Re: [Chimera-users] question about mac laptops / workstations and chimera stability
by Thomas Goddard 05 Feb '07

05 Feb '07

Hi Jeff, I have not seen any graphics driver bug reports with the MacBook Pro with X1600 graphics. I just ordered this machine to replace my four year old Dell with Quadro 4 graphics -- I am confident it will work well using volume data in Chimera. Here is our graphics driver bug page of problems observed with Chimera http://www.cgl.ucsf.edu/chimera/graphicsbugs.html It only has about 1/3 of the driver bugs and I will be adding more from our Chimera bug tracking system when I have time. Tom

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volume path tracer / render surface with marker set
by Jeff 02 Feb '07

02 Feb '07

hello, is there a way to render a surface of arbitrary thickness using a marker set? as in, fit some sort of spline to a marker set, with the constraint being that the algorithm assumes they all lie on the same surface? this would be useful for modeling membranes, perhaps it is already implemented and I am not seeing it in the dialogs. thanks, -J

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Copying volume settings to a second data set
by Thomas Goddard 02 Feb '07

02 Feb '07

Hi Jeff, There is no capability to copy settings (thresholds, colors, brightness, display style, rendering options) that are specific to each volume data set to another data set. That would be useful and I'll add it to the feature request list. Here are some hacks to achieve this. I don't think they are worth the trouble to use but you can decide. If you save a Chimera session with a volume having settings you want to reuse you can edit the session file changing the line: 'path': 'F:\\cygwin\\home\\Tom\\work\\volume\\emd\\emd_1282.map', to 'path': 'F:\\cygwin\\home\\Tom\\work\\volume\\emd\\XXX.map', Then when you reopen that session Chimera will say it cannot find the map file and ask you to select a new map file with a file open dialog. You can choose some other map. The settings from the original map will then be applied to this newly opened map. Another hack is to use the Volume Series tool available on the experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html You can open your maps that you want to use the same settings for as a "volume series". That tool copies settings when you use it to flip between volume in a series. It can even adjust thresholds so they have the same rank position on the histogram (e.g. greater than 94% of voxel values). Tom Jeff wrote: > thanks Tom, > > is there a way to save the thresholds (and color settings) in the > volume viewer, so that when I close a map and reopen a > similar/filtered one, I don't have to re-do all the settings > (brightness and transparency too, for instance) > > i realize the histrogram changes for each map, but even if it saved > how many control points (and their colors) were there, that would > work. is there a 'save volume viewer state' button? I could not find one. > > -Jeff >

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Question on how to represent only chain A of Chimera
by nsomboon＠berkeley.edu 02 Feb '07

02 Feb '07

Hi, I need help. I received the modeling structures of my query (black) and the best representative 1qopB (magenta) through MODWEB, and used Chimera to visualize them (please see attached file). However, the magenta structure also contains 1qopA, in which I only want the 1qopB and don't want the 1qopA. I read through tutorials but cannot find a way to get rid of the chain A of the 1qop. Hence, could you please direct me of how to cut out chain A of 1qop in this attached file? Thank you very much. Sincerely yours, Nara

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Saving modified PDB files
by Bernard Heymann 02 Feb '07

02 Feb '07

I have a problem saving PDB files relative to density maps in recent versions of Chimera. When I load a PDB file and move it relative to a density map, and then try to save it relative to the density map, it does not apply the transformation to the PDB coordinates. This used to work in older versions. My workaround is to have another molecule open and save the transformed one relative to that. However, I would prefer to be able to save a transformed molecule relative to a density map. Can this be fixed? Bernard Heymann, Research Fellow Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH Bethesda MD 20892-8025 Tel. 301-451-8241, Fax. 301-480-7629

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Chimera to visualize MOLDEN-generated VRML2.0 files
by Kalju Kahn 01 Feb '07

01 Feb '07

Dear Chimera users, I am looking for advice on how to make chimera work with VRML 2.0 files generated by MOLDEN. MOLDEN seems to generate valid VRML files (octagaplayer reads these in all right) but chimera crashes with Segmentation fault (core dumped) This happens both on 32-bit Suse 9 system and 64-bit recent Ubuntu system. Any ideas are appreciated! Kalju ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara

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anyone using chimera on a an IBM T43p
by Jeff 01 Feb '07

01 Feb '07

hello, I have an IBM T43p (June '05 or so release) which has an ATI FireGL v3200 (Mobility). In XP, it isn't possible to try out drivers from the vendor, I am limited to drivers from IBM. In Linux, I have been able to install proprietary drivers from ATI, but there is no selection for the 'Mobility' version of the v3200 on ATI's website; the install has not complained though, and basic stuff appears to be fine (GUI is ok, glxgears, etc). In both XP and Linux, chimera will crash when attempting to use volume maps. It appears fine with pdb files, although I typically work with volume data so haven't rigorously tested that. I have been assuming that the FireGL v3200 (Mobility) is the same logic as the v3200, at least documentation I have been able to find seems to imply that. Does anyone know (or suggest) a chimera-stable driver version from ATI that I might test? I might at least be able to get it to work in Linux, as the driver suite downloaded from ATI appears to cover most late-generation cards. thanks for any suggestions, -Jeff

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Re: [Chimera-users] access to pdb parser
by Jean Didier Pie Marechal 01 Feb '07

01 Feb '07

Hi Eric, Well, the truth is that these are two good news. Most likely I didn't explain myself correctly. In reality, for practical reasons, I'd like to use only chimera for the teaching. So, I am planning to only use its internal python shell for python applications. Therefore the tips you gave me are perfect. Thanks a lot for the help! Cheers JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdonyola (Barcelona) Tel: +34.935814988 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Eric Pettersen <pett(a)cgl.ucsf.edu> Data: Dimecres, Gener 31, 2007 10:31 pm Assumpte: Re: [Chimera-users] access to pdb parser > Hi JD, > I have good news and I have bad news. The good news it that using > > PDBio to do what you want is pretty easy. The bad news is that you > > can't use it in a generic Python shell, only in Chimera's own > Python > shell. This is because we use a modified version of Python so that > > the types we define in the C++ layer (Molecule, etc.) can have > attributes added to them in the Python layer -- otherwise they > would > behave like the built-in Python types (dict, list. etc.) that can't > > have arbitrary attributes added to them. We intend to improve our > own code to make modifying Python unnecessary, but haven't gotten > to > it so far. > Nonetheless, you can basically use Chimera in place of a Python > interpreter. "chimera --nogui script.py" will execute the Python > script named script.py without bringing up the Chimera interface. > Also, you can start Chimera normally and bring up the graphical > interface to its interactive Python shell, IDLE (under Tools- > >General > Controls) and type Python commands to that. > Here's a session of me using PDBio in IDLE. I've added some > comments. > >>> from chimera import PDBio # import PDBio > >>> pdbio = PDBio() # create a PDBio instance > >>> mols = pdbio.readPDBfile("/mol/pdb/gc/pdb1gcn.ent") # read a > PDB file given its file name > >>> m = mols[0] # readPDBfile() returned a list of models (NMR > can > have many) so get the model itself > >>> m.pdbHeaders["HEADER"] # each model will have a pdbHeaders > dictionary, keyed by the record type, the values will be a list of > strings -- the PDB records > ['HEADER HORMONE 17-OCT-77 > 1GCN 1GCN 3'] > >>> > > --Eric > > On Jan 31, 2007, at 12:42 PM, Jean Didier Pie Marechal wrote: > > > Hi Eric, > > > > Yes, that would be better to explain more what I'd like to do. > > > > I am planning to give a practical on computational (bio)chemistry > > > in my department next year. I'd stongly like to have the students > > > using chimera and python as their main tools (though both are > tools > > I am in process of learning :-)). > > > > One of the "simple things" I have in mind, is to obtain pdb infos > > > directly from the shell e.g list the SEQRES entry or access to > the > > resolution (REMARK 2), the crystallization conditions etc. The > > students will be chemists and I think that from a didactic point > of > > view, obtaining infos from the python shell would be better that > > reading the pdb files, especially if we want to compare different > > > structures e.g. Writing a comand that gives you ALL the > resolutions > > of the 10 structures you loaded would be interesting. I looked at > > > the PDBio, but I can see how to catch REMARKS infos. > > > > I'd really like to have this work going on, but as you can see, I > > > am a bit lost in where to begin. > > > > Any help to tell me where to start would be fantastic! > > > > Cheers > > > > JD > > > > > > > > > > Dr. Jean-Didier Maréchal > > Professor Lector > > Unitat de Química Física > > Departament de Química > > Universitat Autònoma de Barcelona > > Edifici C.n. > > 08193 Cerdonyola (Barcelona) > > Tel: +34.935814988 > > e-mail: JeanDidier.Marechal(a)uab.es > > > > ----- Missatge original ----- > > De: Eric Pettersen <pett(a)cgl.ucsf.edu> > > Data: Dimarts, Gener 30, 2007 1:25 am > > Assumpte: Re: [Chimera-users] access to pdb parser > > > >> Hi JD, > >> Chimera does its PDB parsing in the C++ layer (the PDBio class in > >> > >> the Python layer). There is a file named PDB.py in the mmCIF- > >> parsing > >> module, but it's not for parsing PDB files. Perhaps if you > >> described > >> why you need Python PDB parsing I could suggest options -- using > >> PDBio possibly being one of them. > >> > >> --Eric > >> > >> Eric Pettersen > >> UCSF Computer Graphics Lab > >> pett(a)cgl.ucsf.edu > >> http://www.cgl.ucsf.edu > >> > >> On Jan 29, 2007, at 1:49 PM, Jean Didier Pie Marechal wrote: > >> > >>> Hello everyone, > >>> > >>> a short question. What is the right call for importing the > >>> pdbparser module in the chimera python shell? I found the PDB.py > >> > >>> module in the site-package mmlib, but I don't know how to import > >> it...> > >>> Thanks a lot, > >>> > >>> JD > >>> > >>> > >>> Dr. Jean-Didier Maréchal > >>> Professor Lector > >>> Unitat de Química Física > >>> Departament de Química > >>> Universitat Autònoma de Barcelona > >>> Edifici C.n. > >>> 08193 Cerdonyola (Barcelona) > >>> Tel: +34.935814988 > >>> e-mail: JeanDidier.Marechal(a)uab.es > >>> > >>> > >>> _______________________________________________ > >>> Chimera-users mailing list > >>> Chimera-users(a)cgl.ucsf.edu > >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >> > >> > > > > > >

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TER Cards and Rainbow Colors
by Albion Baucom 31 Jan '07

31 Jan '07

Is there any way to introduce TER records between breaks in a chain, and still have N->C coloring continuous through a single chain? I have for instance a structure with missing loops that were not observed in density. Therefore there are breaks in the main chain. This is a very common occurrence. To prevent spuriously long bonds I have introduced TER records between the breaks. Then when I apply rainbow coloring from N->C terminus I get the spectral coloring between TER records rather than from the beginning of the chain to the end. I tried the card BREAK, but evidently that is not interpreted by Chimera. Coloring by chain, or by model in the Rainbow panel does not produce the desired effect. Thanks Albion

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Re: [Chimera-users] access to pdb parser
by Eric Pettersen 31 Jan '07

31 Jan '07

Hi JD, I have good news and I have bad news. The good news it that using PDBio to do what you want is pretty easy. The bad news is that you can't use it in a generic Python shell, only in Chimera's own Python shell. This is because we use a modified version of Python so that the types we define in the C++ layer (Molecule, etc.) can have attributes added to them in the Python layer -- otherwise they would behave like the built-in Python types (dict, list. etc.) that can't have arbitrary attributes added to them. We intend to improve our own code to make modifying Python unnecessary, but haven't gotten to it so far. Nonetheless, you can basically use Chimera in place of a Python interpreter. "chimera --nogui script.py" will execute the Python script named script.py without bringing up the Chimera interface. Also, you can start Chimera normally and bring up the graphical interface to its interactive Python shell, IDLE (under Tools->General Controls) and type Python commands to that. Here's a session of me using PDBio in IDLE. I've added some comments. >>> from chimera import PDBio # import PDBio >>> pdbio = PDBio() # create a PDBio instance >>> mols = pdbio.readPDBfile("/mol/pdb/gc/pdb1gcn.ent") # read a PDB file given its file name >>> m = mols[0] # readPDBfile() returned a list of models (NMR can have many) so get the model itself >>> m.pdbHeaders["HEADER"] # each model will have a pdbHeaders dictionary, keyed by the record type, the values will be a list of strings -- the PDB records ['HEADER HORMONE 17-OCT-77 1GCN 1GCN 3'] >>> --Eric On Jan 31, 2007, at 12:42 PM, Jean Didier Pie Marechal wrote: > Hi Eric, > > Yes, that would be better to explain more what I'd like to do. > > I am planning to give a practical on computational (bio)chemistry > in my department next year. I'd stongly like to have the students > using chimera and python as their main tools (though both are tools > I am in process of learning :-)). > > One of the "simple things" I have in mind, is to obtain pdb infos > directly from the shell e.g list the SEQRES entry or access to the > resolution (REMARK 2), the crystallization conditions etc. The > students will be chemists and I think that from a didactic point of > view, obtaining infos from the python shell would be better that > reading the pdb files, especially if we want to compare different > structures e.g. Writing a comand that gives you ALL the resolutions > of the 10 structures you loaded would be interesting. I looked at > the PDBio, but I can see how to catch REMARKS infos. > > I'd really like to have this work going on, but as you can see, I > am a bit lost in where to begin. > > Any help to tell me where to start would be fantastic! > > Cheers > > JD > > > > > Dr. Jean-Didier Maréchal > Professor Lector > Unitat de Química Física > Departament de Química > Universitat Autònoma de Barcelona > Edifici C.n. > 08193 Cerdonyola (Barcelona) > Tel: +34.935814988 > e-mail: JeanDidier.Marechal(a)uab.es > > ----- Missatge original ----- > De: Eric Pettersen <pett(a)cgl.ucsf.edu> > Data: Dimarts, Gener 30, 2007 1:25 am > Assumpte: Re: [Chimera-users] access to pdb parser > >> Hi JD, >> Chimera does its PDB parsing in the C++ layer (the PDBio class in >> >> the Python layer). There is a file named PDB.py in the mmCIF- >> parsing >> module, but it's not for parsing PDB files. Perhaps if you >> described >> why you need Python PDB parsing I could suggest options -- using >> PDBio possibly being one of them. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> pett(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu >> >> On Jan 29, 2007, at 1:49 PM, Jean Didier Pie Marechal wrote: >> >>> Hello everyone, >>> >>> a short question. What is the right call for importing the >>> pdbparser module in the chimera python shell? I found the PDB.py >> >>> module in the site-package mmlib, but I don't know how to import >> it...> >>> Thanks a lot, >>> >>> JD >>> >>> >>> Dr. Jean-Didier Maréchal >>> Professor Lector >>> Unitat de Química Física >>> Departament de Química >>> Universitat Autònoma de Barcelona >>> Edifici C.n. >>> 08193 Cerdonyola (Barcelona) >>> Tel: +34.935814988 >>> e-mail: JeanDidier.Marechal(a)uab.es >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > >

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Re: [Chimera-users] Update volume display without pressing show
by Thomas Goddard 31 Jan '07

31 Jan '07

Hi Jeff, I also wasn't able to reproduce this problem. There is probably a real problem but some step that causes it is missing. If you figure out that step let me know. Tom Jeff wrote: > sorry about the confusion, > > what I meant by 'does not work', is that once I have loaded the volume > planes tool, it appears to not allow me to select 'update display > without pressing show'. (the button is depressed in the dialog box, or > i unclick/reclick it, but it no longer toggles 'update....w/o press > show' on and off). 2318 build. > > sequence: > > 1) load map; display with solid rendering. default is 'update w/o > press show', and you can see the effect of playing with histogram > update in realtime. > > 2) start volume planes. now requires me to press 'show' to update the > display. this also includes other volumes that vol planes is not used > on, and 'update w/o show' no longer works in surface or solid mode. > > 3) close volume planes, or close session. problem persists. > > 4) restart chimera, now it allows 'update..w/o press show' again. > > so, this happened to me twice, and i figured it was just something to > do with the volume planes tool. As I am writing this, I just re-did > the sequence above, and now it works (volume plane tool updates, can > switch to surface). Because I can no longer replicate this, I should > probably be ignored. Also, I just loaded one of the sessions I was > having a problem with into a new launch of chimera, thinking there > might be some sort of 'system/state snapshot' I could send you, but > now it is working too. So, it appears to have been fixed by a restart > of chimera. Again, please ignore. > > -Jeff

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Re: [Chimera-users] Update volume display without pressing show
by Thomas Goddard 31 Jan '07

31 Jan '07

Hi Jeff, I tried the volume "update show" option in combination with volume planes and did not find an problem. Can you give me step by step instructions to produce the problem? Also I don't know what you mean by "does not work". Does it always update automatically, or never update automatically? What Chimera version? With the volume planes tool, the full map is still opened -- it is just display a subregion that is 1 plane high. Use Features / Region Bounds to see and change the subregion. Or use Features / Subregion Selection and press the Full button to get back to the full map. Also the volume planes dialog always acts on the volume displayed in the volume dialog. Perhaps it should have its own menu to choose the volume you want to show planes for. Tom Jeff wrote: > even if I close the volume planes tool, > > 'update display without pressing Show' no longer works (for instance, > adjusting the volume rendering histogram, or clicking 'surface' > rendering). if I close, then re-open the volume, it still doesn't > work. bug, or my version maybe? > > also, once you start 'volume planes tool', it only keeps track of the > plane it has pulled from the volume map - what used to be a > 100x100x100 volume is now 100x100x1; the volume viewer 'renames' the > map but does not save it out that way (which is good). is there a way > to be able to keep the full volume around, but not displayed? there > are reasons you might want to do that (well, I found myself trying to > do that), without having to re-open the volume. > > i did check to see if i could open 2 copies - one first to run 'volume > planes' on, and then one to subsample but have as a volume rendering, > for example. this works, as long as i don't accidentally touch the > 'volume planes' dialog when fooling with the second opened copy of the > volume. > > mainly just curious, not asking for additional functionality, just > wanted to let you know what I was trying and why. > > -Jeff > > > > Thomas Goddard wrote: >> Hi Jeff, >> >> The volume dialog data display option "Update display without >> pressing Show" only effect volume dialog features. It does not have >> any effect on the Volume Planes tool. The Volume Planes tool does >> not allow adjusting the plane number without updating the display. >> >> Tom >> >> >> Jeff wrote: >>> hi Tom, >>> >>> I have volume planes and precomputed subsamplings going, and the >>> 'update display without pressing Show' no longer works (keep >>> toggling on and off, but it doesn't have an effect) >>> >>> is there a way for me to 'refresh' the state of buttons like that? >>> >>> -Jeff >>

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Watershed segmentation of volumes
by Thomas Goddard 31 Jan '07

31 Jan '07

Hi Jeff, There is no watershed or flood-fill type of method in Chimera for segmenting volume data. This is on our (very long) list of features to develop though. Tom Jeff wrote: > tom, > > i hate to keep piling on questions, but how hard would it be to have a > feature where one places a chimera marker, and then has some sort of > algorithm expand to 'fill' the space, kind of an isosurface problem > (or does this already exist) > > i have 'voids' in some of my maps (stained sections) which i think > correspond to protein, like one sees in negative stain (the positive > values/density in the map correspond to stain; an enclosed void > (density more or less = 0 or close to it) is thought to represent the > actual protein, which was covered in stain, kind of like 'magic shell' > on ice cream - or think of dairy queen cone, dipped in chocolate that > then solidifies), and would like some way to 'grow' a blob in the void > (or at least try) > > does this already exist? i have a buddy who does level set methods who > is often looking for ways to use his library, but i thought i should > ask you first if there is some functionality like this > > -jeff

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Quadro FX 1400/3450 performance
by Thomas Goddard 31 Jan '07

31 Jan '07

Hi Maya, It must be exciting and alot of work to get your lab running. Glad to hear you are making Chimera converts. Graphics benchmark scores using Chimera with the quadro fx 1400 and quadro fx 3400 are shown here http://www.cgl.ucsf.edu/chimera/benchmarks.html We don't have any numbers for the fx 3450 and I don't know if it is similar to the 3400. The 1400 and 3400 have very similar Chimera scores. The Chimera scores indicate how big a test volume can be handled at 10 frames per second. Both these cards are very fast. The one difference I see is that on the Nvidia web site they say the 1400 has 128 Mbytes of memory while the 3450 has 256 Mbytes. http://www.nvidia.com/page/qfx_mr.html http://www.nvidia.com/page/quadrofx.html (fx 3400) Maybe that info is out of date -- maybe there is a choice of memory size. On the Chimera page the fx 1400 had 256 Mb. And 128 Mbytes is small by today's standards. 256 Mbytes is common, and 512 Mbytes is available with some cards. The amount of graphics memory is most noticable if you use the Chimera "solid" rendering mode because it tries to put red,green,blue 8-bit values for the entire volume on the card. For 256^3 volume that is 48 Mbytes, or if you use Chimera 2-D textures mode (the default) it take 3 times that (144 Mbytes). It can also make a difference for very large contour surfaces -- ones you might use for making a figure but would be too slow for interactive rotating (e.g. 10 million triangles at about 18 bytes per triangle = 180 Mbytes). Regarding stereo, I'm not sure if there are any flat panel displays that can work with the LCD glasses. They don't refresh fast enough so there is too much flicker. So you either need a CRT display or maybe some special high-end flat panel. See you at the EMAN workshop. Maya Topf wrote: > Hi Tom, > > How are you? > I am slowly settling down in the UK. Lots of work and collaborations. > A few people from the EM group at birkbeck started using chimera and > they really like it! > > I have a question about graphics cards and maybe you can help me. > I am thinking about buying either NVIDIA QUADRO FX 1400 (stereo) or FX > 3450 (stereo). > Do you think that there is a big difference when I want > to visualise large maps with chimera for example? > > thanks, > Maya > > I saw that you are coming to the eman workshop so I guess I will see > you there! > Tom

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ViewDock descriptors problem
by "Воронков андрей" 31 Jan '07

31 Jan '07

Dear Chimera users, I have ranked database from DOCK. I need to see energies of these structures and their ranking. I open them by View Dock, but in the field Column menu I can see only name field. Why I don't have energy field there and how can I get it? Respectively yours, Andrew PS "Descriptors can be shown in or removed from the upper panel using the Column menu." -this is from manual, but I can;t make shown any descriptos but the name of the structure

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Re: [Chimera-users] using a marker file to zone a volume from python prompt
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, I added a user interface dialog for rotating and translating atom coordinates. Markers in Chimera are equivalent to atoms so it works on those. The rotation is specified in Euler angles. The new dialog, called Transform Molecule Coordinates, is available on the experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Tom Jeff wrote: > thanks Tom, > > much appreciated. how hard is it for me to write a dialog GUI to provide > 3 numerical inputs to the rotation script you forwarded me? (is it more > involved than a few lines? I am not familiar with Tkinter). > > don't want to bother you too much, if it is not a quick thing/response > feel free to punt, please. > > -jeff >

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Update volume display without pressing show
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, The volume dialog data display option "Update display without pressing Show" only effect volume dialog features. It does not have any effect on the Volume Planes tool. The Volume Planes tool does not allow adjusting the plane number without updating the display. Tom Jeff wrote: > hi Tom, > > I have volume planes and precomputed subsamplings going, and the 'update > display without pressing Show' no longer works (keep toggling on and > off, but it doesn't have an effect) > > is there a way for me to 'refresh' the state of buttons like that? > > -Jeff

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Re: [Chimera-users] Representation of volume data in memory
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, I suspect 2-byte integers are not faster to access or compute with then 4-byte floats on modern CPUs. But more of the map will fit into the CPUs cache which could improve bandwidth and could make computing a contour surface faster. But I don't think that will be significant. You would need to test it to know. Chimera keeps the native data type of the map to conserve memory when reading large maps. Tom Jeff wrote: > does this mean that a 2-byte integer format of a file will display > faster / render triangles faster than the equivalent sized 4-byte float > map? > > Thomas Goddard wrote: >> Hi Jeff, >> >> Chimera keeps volume data in memory using the same numeric value >> types that are present in the file, for example, 32-bit float, 16-bit >> integer, 8-bit integer. >> >> Volume data is copied only when necessary -- for instance, using the >> Gaussian Filter tool creates a floating point copy of the data since >> Gaussian convolution of integer data produces a floating point result. >> >> Tom >> >> >> Jeff wrote: >>> does chimera store all values as float internally (even if the >>> original map is in 2 byte integers), making the mode of the MRC file >>> irrelevant to chimera's performance? >>> >>> -jeff >>

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Re: [Chimera-users] zone tool and volume rendering
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, The Chimera handling of the MRC file origin position is done in Python code chimera/share/VolumeData/mrc/mrc_format.py In summary, if it is an MRC2000 file (ie has xorigin, yorigin, and zorigin header values) then (xorigin, yorigin, zorigin) is used as the xyz coordinates of the volume index (0,0,0) unless xorigin, yorigin and zorigin are all zero in which case the xyz position of the map index (0,0,0) is calculated using integer (ncstart, nrstart, nsstart) header values times the grid spacing (defined by (xlen/mx,ylen/my,zlen/mz)). It is never the case that both (ncstart,nrstart,nsstart) and (xorigin,yorigin,zorigin) are used in positioning the map. Tom Jeff wrote: > > I often use another tool to cut out subregions, that I then load into > chimera - until you told me recently, I did not know I could pre-load > subsampled maps, or be able to keep a 'subsampled overview' present > while selecting various regions > > when using other tools to cut out these smaller areas (either IMOD or > Priism), some tools record displacements, and some don't. the Priism > 'CopyRegion' tool appears to do this by adjusting the 'start pixel' > field in the MRC header. IMOD doesn't do this. the 'copyRegion' tool > also doesn't appear to transfer well to chimera, at least in my test > case the original and subvolume do not register properly. (I don't have > any expectation that it would work properly, but I would adapt if I knew > what chimera expects.) > > I am also not sure what entries chimera uses to keep track of > displacements when it cuts out volumes (I could do that experiment right > now), whether it uses 'start pixel' or 'origin', if 'origin' is recorded > in Angstroms or pixels, etc. Also, I don't know what chimera considers > the origin of a density map - if 'start pixel' is 10,10,10, the map is > 20x20x20 pixels in dim, and the origin is (0,0,0), is the origin at the > center of the map, or at the 0,0,0 pixel coordinate of the map? I have > been assuming that 'origin' has to refer to the map's origin location in > space, but this requires defining where the origin is in the volume map > (I think). if there is a 'start pixel' entry, does this effectively > shift the origin? As an example, if the pixel res is 10 A, will the map > example above now display starting at (10 A, 10 A, 10 A)? Or, is one > (or both) of these entries ignored? Finally, if there is already an > entry in one of these fields, does chimera respect that and just > increment, or does it clobber it with the relative displacement > calculated when excising a subvolume? (this slew of questions is > probably covered by a single answer, but I thought it would be good to > elaborate) > > If I knew, I could more appropriately jump between programs. As I am > writing this, I just got an email from David at Boulder telling me that > IMOD uses the origin entries in the header (but don't know yet what it > considers to be the origin, 'far left' corner or center or something else). > > -Jeff

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Precomputing subsampled map sizes
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, Yes, Chimera will complain and not allow precomputed volume subsamples if the size of the subsample grid is not what is expected. In the case you give (1434,1434,110) with subsample grid of size (358,358,26) the subsample grid size is not acceptable. Notice that 4 times the subsample size is (1432, 1432, 104) So a half size bins in the first two dimensions are left off (1434 - 1432 = 2) -- that is fine. But the third dimension is missing 1.5 bins (110 - 104 = 6). The subsample file should have size 27 in the third dimension, ie (358,358,27). I don't know why squeezevol from IMOD dropped off more than a whole bin in the third dimension. Chimera allows fractional bins to be dropped off, but does not allow whole bins to be missing. Tom Jeff wrote: > hi again, > > is there a problem with the precomputed subsamplings needing even > dimensions (I pre-cut my volume to even dimensions so that a binning of > 2 would result in a whole number for the subsampled dimensions, but it > can be hard to do this for a factor of 8 in advance). > > chimera is complaining to me about bad dimensions ('Data foo.mrc of size > (358,358,26) not a valid size for dubsamples of foo.mrc of size > (1434,1434,110). > > is there a program you use to bin / get around this problem? I use > 'squeezevol' from IMOD, I am not sure if it is completely transparent in > its output for what chimera would expect > > -j

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Representation of volume data in memory
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, Chimera keeps volume data in memory using the same numeric value types that are present in the file, for example, 32-bit float, 16-bit integer, 8-bit integer. Volume data is copied only when necessary -- for instance, using the Gaussian Filter tool creates a floating point copy of the data since Gaussian convolution of integer data produces a floating point result. Tom Jeff wrote: > does chimera store all values as float internally (even if the original > map is in 2 byte integers), making the mode of the MRC file irrelevant > to chimera's performance? > > -jeff

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