- Chimera-users - RBVI Mailing Lists

transparent surfaces
by Charles Midgett 05 May '08

05 May '08

I want to make a transparent surface in volume viewer that can be drawn in POVray. It appears the *.pov and *.ini files produced by Chimera cannot be read by other POVray renders. Is there some work around that will allow me to ray trace a transparent surface displayed by the volume viewer? Charles

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areaSAS_areaSES
by De Nicola, Gian 05 May '08

05 May '08

To whom it may concern I would like to calculate the areaSAS and areasSES using Chimera.This is what I do Load the structure tools Surface Binding Analysis area/volume from web I choose the type of surface I want. Click apply then Ok As an output I get " unexpected output from struc tools server" . What am I doing wrong? Regards Gian

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surfaces, electrostatic coloring
by Elaine Meng 03 May '08

03 May '08

On May 2, 2008, at 8:04 PM, James Fethiere wrote: > > Another wquestion. I managed to display separate surfaces for 2 > chains in a single model using the surfcat command you've > recommended last time. Is this command accessible through the menu? There is no menu equivalent to "surfcat," sorry. > > However, I can't color each surface separately according to > electrostatics. I know that chimera does not calculate > electrostatics. What I tried is to go to tools/surface binding/ > electrostatic surface coloring, set the palette to radius and set > the full range. What I get when I color is a gradation from red to > blue with no atom type discrimination. When you choose "radius" the coloring is by distance from a point, not electrostatics.. To actually color by electrostatics, you would have to open an electrostatic potential map and then choose it from that menu (the one with "radius" in it). Also, your two surfaces would be two separate entries in the menu listing the surfaces. You would have to choose one, color, and then choose the other, color again. Perhaps it is misleading to call this tool "Electrostatic Surface Coloring" when it is really identical to the "Surface Color" tool: it includes options to color by distance from a point, axis, or plane. The radial coloring is used (for example) to color a virus capsid by the distance from its center to highlight the contours of its surface; see the figure in the man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ surfcolor.html Another possibly confusing thing is that in older versions of Chimera, after you use Surface Color, it can be tricky to change the color of the surfaces. In current versions (recent daily builds), you should just be able to color the surface with the menu (Actions... Color) or commands (color, rangecolor) regardless of whether this tool had been used. > So I go to the attributes of this map in the model panel, and color > source atoms. Great, I get red for acidic and blue for basics. > Now for the other chain, it doesn't work. At the color source atoms > step, the whole surface takes one single color. The other thing is > that in the model panel I do not have the small color icon for the > two maps!! Is there a better way to do this? The two surfaces would again be listed separately in the Model Panel, and have their own separate attributes dialogs. I don't know what you mean by "doesn't work." Did you try to use the menu or commands to color the surface? Also, I don't know what other things you did in the session, but the red and blue you were seeing were probably just the element colors: surfaces of oxygen atoms (red) and nitrogen atoms (blue). Maybe you had colored the atoms of one chain and not the other. In any case, you could proceed to color the surfaces with the menu and/or commands as mentioned above. If you don't have an electrostatic potential map and don't want to color by distance from a point, axis, or plane, there is no reason to use Surface Color. For example, to show the element colors on the surface for the two chains in 2zcp: open 2zcp surfcat one :.a & protein surfcat two :.b & protein surf one surf two col byatom (or "col byhet" to not change carbon color) Or, instead of using the atomic element colors, you could color :asp,glu residues red and :his,arg,lys residues blue. > > Can you also tell me how to make the surfaces smoother. Whatever > vertex density I give, I see pretty rough edges and it's not very > nice. The vertex density is the only way I know of for making the surface smoother. I am surprised it is not doing that in your case - it definitely works in the molecular surfaces I have tried: 5.0 is a lot better, 10.0 even better. Did you press return? The main drawback I ran into is that it can take a long time to calculate, rotate, etc. Maybe increasing the probe radius would improve your surface's appearance. I hope this helps, Elaine

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Sec structure loss
by James Fethiere 02 May '08

02 May '08

Hi, I'm seing something strange with secondary structure assignments in peptides. Two examples: PDB 1axc has a peptide bound to PCNA with beta strand interactions and chimera doesn't pick it up as a strand. In the other example, 1rxz, it picks up the strand in a similar peptide but the strand disappear when I run matchmaker with 1ul1 (which also has a strand at the c-terminus that is not picked up. Is there any explanation? Are the criteria for secondary structure assignments to strict? One more thing that may have been asked already!! how does one keeps the NH and CO of the peptide bond displayed in the ribbons view? Thanks James

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automated rebuilding of side chains?
by Ian Yarbrough 02 May '08

02 May '08

Hi, A model that I am working with has several missing or partial side chains, and I'm dealing with about 80 subunits of this protein (organized into 3 chains). I am trying to repair these, but don't want to go through the task of finding every broken chain. Is there a way to get chimera to locate the broken ones and repair them all? I've seen the dock prep feature, but don't want to change them all to alanines. Thanks for you help. Ian Yarbrough Texas A&M University

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adding metal ions
by Carlo Zambonelli 01 May '08

01 May '08

I have a pdb file with the coordinates of an apo-enzyme. I know Fe3+ and Zn2+ are essential for catalysis; I also know some of the residues involved in coordination of Fe3+ and Zn2+. Can I position 2 ions in the structure so that they are correctly oriented relative to the coordinating residues? My ultimate goal is to create a PDF file containing also the metal ions. Thanks, Carlo

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adding metal ions
by Carlo Zambonelli 01 May '08

01 May '08

I have a pdb file with the coordinates of an apo-enzyme. I know Fe3+ and Zn2+ are essential for catalysis; I also know some of the residues involved in coordination of Fe3+ and Zn2+. Can I position 2 ions in the structure so that they are correctly oriented relative to the coordinating residues? My ultimate goal is to create a PDF file containing also the metal ions. Thanks, Carlo

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Moving an ensemble of molecules together
by Thomas Goddard 01 May '08

01 May '08

Hi Miguel, If you have two molecules each surrounded by additional molecule copies that make crystal contacts you can align the two crystal lattices as follows. Align the two original molecules (e.g. using Match Maker dialog or match command). Then choose all copies of the first molecule in Model Panel and use the Transform As button. You'll be asked to choose the molecule to transform these as, so choose the aligned molecule. That will bring all the crystal contact molecules surrounding the aligned molecule into correct locations around the aligned molecule. This method assumes you have saved the crystal copies to a PDB file and have opened that file. If you simply use the new crystal contacts option to make the molecule copies then the Transform As will move all those copies to the exact same position as the original molecule -- not what you want. This is because the crystal contacts tool is placing the surrounding molecules by adjusting their transformation matrices rather than changing their atom coordinates. If you save all copies to a PDB file and read it back in then the atom coordinates of the copies will be adjusted and all of the molecules will have the same transformation matrix and the above alignment procedure will work. Tom Miguel Ortiz-Lombardía wrote: > Hi again! > > I had tried this, yes. But the problem is that when I want to compare > crystal packings the procedure is: > > 1. Generate the two ensembles around "central" molecules > 2. Superpose the "central" molecule (submodel if saved as you say) of > the first ensemble to the "central" molecule of the second one > > Doing it this way only the central submodel of the first ensemble moves, > not the whole ensemble, as I wish... A single molecule with various > chains would move as a whole, as I want. I see the 62 chains limitation, > but normally we don't have such enormous amount of molecules contacting > an asymmetric unit (of course, with viruses may be different). So, it > would be nice (to me, I don't know how generally) to have a way to > transform an ensemble of models into an ensemble of chains. > > Thank you for your help! > > > Miguel > > 2008/4/30 Tom Goddard <goddard(a)cgl.ucsf.edu <mailto:goddard@cgl.ucsf.edu>>: > > Hi Miguel, > > You mentioned that you would like to be able to save the crystal > contact asym units in a single PDB file as separate chains. Why not > save them as multiple models in a single PDB file? You can do this > currently with the Chimera menu entry File / Save PDB.... Making > separate chains requires making new chain names and since only one > letter names are allowed in PDB format this is limited to about 62 > chains (a-z, A-Z, 0-9). > > Tom > > > > > -- > http://www.pangea.org/mol/spip.php?rubrique2 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Je suis de la mauvaise herbe, > Braves gens, braves gens, > Je pousse en liberté > Dans les jardins mal fréquentés! > Georges Brassens

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pretty nice article on PDB website about Chimera
by Eric Pettersen 30 Apr '08

30 Apr '08

http://www.rcsb.org/pdb/general_information/news_publications/ newsletters/2008q1/education_corner.html

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Initial window size
by Bernard Heymann 30 Apr '08

30 Apr '08

Where is the initial graphics window size set? I did not see any preference for that. I would like to change that to have Chimera open with a bigger window. Thanks Bernard Heymann Rm 1515, 50 South Dr, NIH, Bethesda, 20892-8025 Tel 301-451-8241, Fax 301-480-7629

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Can I re-save the mol2 file of compounds sorted by grid score?
by �� 29 Apr '08

29 Apr '08

Hi there, I'm a novice in Chimera. I have done the ViewDock tutorial, but now I have a question. I know, in the ViewDock, the listing can be sorted by any column(e.g. Grid Score). And I expect to know if I could re-save the mol2 file of the compounds sorted by grid score. Any answer would be appreciated! Best regards, Yolanda Guo Northeast Normal University --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.

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Calling Chimera from another program
by Tom Goddard 29 Apr '08

29 Apr '08

Hi Brian, I talked to Niels Volkmann on Friday about how PyCoan can use Chimera for displaying maps. There are two existing ways for programs to communicate with Chimera. Here are some info about those. Since PyCoan uses Python it would be possible for it to run under the same Python interpreter as Chimera. Current Chimera daily builds use a standard Python 2.5 distribution with a bunch of additional modules (numpy, pil, pytables, ...) included. Although this approach gives the most power for passing data between PyCoan and Chimera, it requires the two programs to use exactly the same versions of third party Python modules and that can cause problems. Also it allows unlimited access to Chimera internals and use of that functionality would likely make PyCoan/Chimera communication break as Chimera code evolves. There are two ways to communicate with Chimera from a separate process. One involves sending Chimera commands (e.g. "open mymap.mrc") to Chimera's stdin. You have to start Chimera with the following option to get it to read stdin "chimera --start ReadStdin". The other method involves sending Python code to Chimera using a socket. The second approach works by running "chimera --send somecode.py" which will connect to an existing Chimera on the local machine or start one if none is running. Both methods require Chimera and the controlling process to run on the same machine. The second method does not require that limitation but we impose it because there is no authentication method -- so if you allow remote connections, anyone could run arbitrary Python code on your machine (unlikely to be abused, but we're not going to distribute that capability). The first approach is limited to Chimera commands and many Chimera capabilities available in the graphical user interface have no equivalent command. All the capabilities are available if Python code is used. Sending Chimera commands returns the text output of the command although this rarely contains useful information. Sending Python code with "chimera --send xxx.py" returns nothing. So the communication is essentially uni-directional. The advantage of these communication methods over just start Chimera with a Python script as an argument is that you can maintain a connection to a single instance of Chimera and update the visualization as needed. Both the stdin and socket methods need map data to be written to a separate file if you want to open that. Niels was interested in avoiding the use of temporary files and suggested using shared memory. Python has some shared memory support but I recommend against that. The performance is unlikely to be dramatically better. If you write a temporary file the operating system is going to cache it in memory rather than writing it to disk and Chimera will then read it from memory. If you delete the temporary file soon it may never be written to disk. You could force this behavior using shared memory but that is just a more complex way to achieve the same optimization that the operating system is already providing. In any case I would not pursue that until you test the performance of using files. I've attached an example Python script that starts Chimera and sends commands to open a volume and set its contour level and color. I tested it with a Chimera daily build (1.2502). I recommend using the daily builds instead of the November 2007 production release since many volume data improvements have been made. Here is Chimera documentation on the ReadStdin and "--send" communication methods. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/readstdin/readstdi… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html Tom # ----------------------------------------------------------------------------- # Example program that sends commands to Chimera. # class Chimera_IO: def __init__(self): args = ['chimera', '--start', 'ReadStdin'] self.prog = run_program(args) def send_command(self, command): p = self.prog p.stdin.write(command + '\n') p.stdin.flush() # Collect output. lines = [] while True: line = p.stdout.readline() if line == '' or line == 'END\n': break lines.append(line) output = ''.join(lines) return output # ----------------------------------------------------------------------------- # def run_program(args): # Hide console window on Windows. import sys if sys.platform == 'win32': from subprocess import STARTUPINFO, STARTF_USESHOWWINDOW spinfo = STARTUPINFO() spinfo.dwFlags |= STARTF_USESHOWWINDOW else: spinfo = None from subprocess import Popen, PIPE try: p = Popen(args, stdin = PIPE, stdout = PIPE, startupinfo = spinfo) except: print 'Starting "%s" failed.\n' % ' '.join(args) return None return p # ----------------------------------------------------------------------------- # c = Chimera_IO() print c.send_command('open 0 /tmp/sfv.mrc') print c.send_command('volume #0 level 2500 color tan')

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crystal contacts to show molecules
by Miguel Ortiz-Lombardía 28 Apr '08

28 Apr '08

Dear all, Would it be possible to modify the code of the Crystal Contact tool so it can produce, as an option, the molecules that are in contact with the model as full atom models instead of spheres? I would be happy to do so, but then I would appreciate if you can point me to the relevant code in chimera to do so. Thank you! Miguel -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

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post-processing of Chimera images
by Jonathan Hilmer 28 Apr '08

28 Apr '08

Francesco: Especially since you're preparing images for publication, I would recommend you use software such as Inkscape (a excellent free alternative to Adobe Illustrator) to handle the composition of figures. It's a vector-based program that's much better suited to handling geometric shapes as compared to a raster program like Photoshop or Gimp. The final post in the following discussion has a good overview with screenshots showing how Inkscape can be used: http://inkscape-forum.andreas-s.net/topic/146897 Here are some of the screenshots: http://jo.irisson.free.fr/dropbox/inkscape/poster_inkscape_style2.png http://jo.irisson.free.fr/dropbox/inkscape/poster_inkscape_outline.png I've got an example figure that you can see that uses some of the basic features with images, shapes, figures, and text: ftp://guest:@bothnerlab01.chemistry.montana.edu/inkscape_example.zip The best part of using Inkscape is that it's totally resolution-independent, so you can export graphics for publication at whatever resolution or format is required. There are only two disadvantages to Inkscape that I have found so far. First, the PDF export option works fine but treats text as shapes, so the resulting files are huge if there is substantial amounts of text: ~500MB for a poster with about 50% text. Second, it doesn't embed images within the saved files the way Powerpoint does: it just saves links in the manner of OpenOffice. I rather prefer that behavior, but you have to be prepared for it if you're moving files around. Regardless, once you give it a try you'll never go back to using Powerpoint or Photoshop for making figures or posters. Jonathan On Mon, Apr 28, 2008 at 1:00 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Numbering the amino acid sequence (Jeff Speir) > 2. Re: Chimera - Matchmaker tool (Elaine Meng) > 3. Re: Numbering the amino acid sequence (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 28 Apr 2008 09:07:02 -0700 > From: Jeff Speir <speir(a)scripps.edu> > Subject: Re: [Chimera-users] Numbering the amino acid sequence > To: chiendarret(a)yahoo.com > Cc: chimera <chimera-users(a)cgl.ucsf.edu> > Message-ID: <B2AD9487-6EEF-4AC4-8060-51788F8E86B2(a)scripps.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Outside of Chimera, there are several ways to do this in image > editing programs (Gimp, Photoshop, etc.). Use layers and: 1) draw > arrows; or 2) place the number on top of a box just big enough to fit > the text (opaque to semi-transparent); or 3) use effects on the text, > such as adding an outer glow effect in Photoshop, which adds a halo > around the text so that its outline stands out from the image, making > it readable. > > I would advise not going crazy with colors, this just adds to the > complexity of the image. > > Cheers, > > Jeff > > > > On Apr 27, 2008, at 10:49 AM, Francesco Pietra wrote: > > > A referee is asking me to number the amino acid sequence involved > > in docking a ligand with a protein. Not satisfied by having a side > > table with a guideline. > > > > Is it possible to add that numbering in a least-intruding way? The > > figure exported in standard graphic formats from Chimera is already > > extremely crowded. Therefore, is any possibility of adding the > > numbering outside the protein with some kind of pointers? I can't > > do with colors alone: I already used different colors for different > > helices. > > > > Thanks > > francesco pietra

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Numbering the amino acid sequence
by Francesco Pietra 28 Apr '08

28 Apr '08

A referee is asking me to number the amino acid sequence involved in docking a ligand with a protein. Not satisfied by having a side table with a guideline. Is it possible to add that numbering in a least-intruding way? The figure exported in standard graphic formats from Chimera is already extremely crowded. Therefore, is any possibility of adding the numbering outside the protein with some kind of pointers? I can't do with colors alone: I already used different colors for different helices. Thanks francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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Re: [Chimera-users] Chimera - Matchmaker tool
by Elaine Meng 28 Apr '08

28 Apr '08

On Apr 27, 2008, at 10:16 AM, Sujata wrote: > Hi, > I am using Chimera for awhile now to analysis modeled structures > and I love it, way better for visualizing than a lot of other > softwares and very user freindly. > I do have a question about Matchmaker- is there a way that I can > get the total number of atom-pairs in the 'matchlist' it generates > in Matchmaker? Or in other words, I want to know the final > percentage of atom-pairs that Chimera gives me after pruning the > long atom pairs that do not exceed 2 Angstroms to compute the RMSD. > > Thank you very much. > Sujata Sovani > Hi Sujata, Thanks, tell your friends! 8-) The final match RMSD and number of alpha-carbon pairs are reported in the Reply Log (under Favorites). They are also shown in the status line at the bottom of the Chimera window, but only temporarily. If you also show the sequence alignment from MatchMaker, these residue pairs used in the final fit iteration are shown in boxes with orange- red outline and light orange interior. I am not sure which percentage you wanted; one possibility is to divide by the total number of residues in a structure. You can also find out how many pairs were pruned by doing another match with the same parameters except without iteration. That does not change the sequence alignment, only the fitting. If you already showed the sequence alignment from matchmaker, you wouldn't have to rerun matchmaker, only choose Structure... Match from the sequence alignment window and apply it with all its options turned off. 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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Independent model rotation
by Eduardo Sanz Garcia 26 Apr '08

26 Apr '08

I have a little request (I don't know if it would be feasible). I always work with several models at the same time. I would like to set the the default center of rotation as "independent". It seems that the "Save" button in the following panel (attached image) should do it, but it is not. Is there a way to implement this option? Thank you very much.

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questions on find hbond, find clashes/contact
by Harinathachari Bahudhanapati 25 Apr '08

25 Apr '08

Dear chimera support, I am a huge fan of chimera and I have so say I spend a lot of time on chimera these days, as a part of writing for my dissertation. I have a few questions and I sincerely you to request to help me out. 1. About findHbond: I never seem to get this one right. I model Enzyme-inhibitor complexes on patchdock. The inhibitor templates are either pdbs from rcsb or modelled on swissmodel. I am not able to locate or find any hbonds newly formed in the docked models, when I search for intermodel hbonds (I am looking for protein-protein interactions). Are there any special criteria or am I missing some thing? I want something similar to that of the output of HBPLUS (I never seem to get this working either - very frustrating) 2. About find clashes: What are the ideal parameters for clashes and contacts. I tried several things, they give me several no of overlaps for several different parameters. Are these vanderwaals interactions? because some times I see more than 40 interactions between two residues -i.e., between the atoms of Enzyme and inhibitor? How reliable are these interactions (I need to publish my data) This tool does not seem to work unless I add hydrogens to both the chains. 3. It would be great, if there was a energy minimization tool in chimera because I introduce mutations. Please kindly suggest me if there are any easy to use tools for this. I tried COOT and swisspdbviewer, but not really that user-friendly. I read all the newsletter e-mails from CHIMERA users-list everyday. Thanks to Elaine, tom, eric and conrad. You guys rock.. sincerely Hari hbahudha(a)fau.edu

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correlation plot
by bala 25 Apr '08

25 Apr '08

Dear chimera friends, I have a simulated trajectory of a RNA molecule. I want to make a correlation plot based on residue fluctuation. I am new to scritping in python. Can anybody please give me some suggestions or any sample script for such analysis if possible. Regards, Bala

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PDF Chimera documentation
by Elaine Meng 25 Apr '08

25 Apr '08

Hi everybody, For those of you who have asked about a PDF version of the documentation: we just made PDFs of the User's Guide and Programmer's Guide for the last production release (1.2470 Nov 2007). These are linked near the bottom of http://www.cgl.ucsf.edu/chimera/docindex.html (the page you get from clicking "Documentation" in the lefthand column of the Chimera home page). ** HOWEVER, these files have several limitations: - large size (User's Guide >600 pages, Programmer's Guide >2600 pages!) - suboptimal page ordering due to the nonlinear nature of the documentation - some redundancies, i.e., pages occurring more than once in the PDF document Because of these limitations, we recommend using the documentation in HTML form where possible, and printing from your Web browser to obtain hard copies of specific parts as needed. Also, the HTML documentation is updated constantly, whereas the PDF files may not be updated very often. 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

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Benchmark scores
by Sacha De Carlo 25 Apr '08

25 Apr '08

System : DELL Inspiron 530s, WinXP, 3Gb @ 800MHz Graphics : Radeon HD 2400 Pro 256Mb DDR3, driver version 6.14.0010.6764 Proc: Intel Dual E2160(a)1.8GHz Test date: 2008/4/25 Benchmark scores surface 648 mesh 554 contour 168 solid 248 recolor 115 Molecule Benchmark scores 1F4H (33805): 93.0 171.0 8.0 7.0 173.0 14.0 30.0

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Tile 3D EM maps
by Eduardo Sanz-Garcia 24 Apr '08

24 Apr '08

I found that "tile" only works with atomic coordinate models. Is there a way to "tile" 3D EM maps? Thank you

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Morph surfaces
by Thomas Goddard 24 Apr '08

24 Apr '08

Hi Craig, You can make a low resolution surface from atomic coordinates using the new molmap Chimera command (added in January 2008). You can create such a surface for each frame of your morph using the MD Movie dialog menu entry Per-Frame / Define Script. If your morph is model #2 the script would look like: molmap #2 8.5 where 8.5 is the desired resolution in Angstroms. To produce a smoother surface, to color it (transparent red), and to set the volume step size (the surface is a contour surface of a map computed from the molecule) the script would look like molmap #2 8.5 gridSpacing 1.5 volume #2 color 1,0,0,.5 step 1 The color spec is red,green,blue,opacity. The molmap command replaces a previous map for the molecule by default so the surfaces will not accumulate. More details on the molmap command are in the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html You'll need a Chimera daily build to use this command: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom Craig Yoshioka wrote: > Hi Dr. Goddard, > > I'm Craig, a graduate student in Clint and Bridget's lab at Scripps. I > am trying to use Chimera to put together an animation movie. I have > fitted a couple of crystal structures into different EM maps and have > used the Morph Conformations to interpolate between them (excellent > btw). I want to do the animation using surfaces though, and have not > found a satisfactory way to do so. The surfacing command under the > actions menu seems to fail half the time, but provides far too detailed > a surface for this animation anyways. I really like the flexibility of > the surfacing used by the multi-scale model window (letting you set the > "resolution", etc.) but this surface does not update with the morph > conformations animation. I have taken to saving the morph conformations > pdb to the disk as all frames, and reopening it to get access to all the > intermediate PDBs. I then using multi-scale surfacing on this to > generate a large series of surfaces, and I generate the animation by > switching them on and off in series. This is, of course, very time > consuming. Is there a way for me to switch the algorithm used by the > surfacing in the actions menu to use the multi-scale models surfacing > instead? That way the animation would be much easier. > > thanks for your help, > > -Craig > >

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chimera on OS X 10.5
by Mark Moll 23 Apr '08

23 Apr '08

When I run Chimera on OS X 10.5 "Leopard", I get a ton of the following errors in /var/log/system.log: The process has forked and you cannot use this CoreFoundation functionality safely. You MUST exec(). Break on __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__ () to debug. I first reported on this on November 2, 2007, but with the latest daily build this still happens. I removed all extensions, but that doesn't seem to make a difference. My own extension becomes painfully slow, because Chimera is constantly writing the above error message. I never get the error above with the version of python that comes with Leopard or with the version of python2.5 in MacPorts. Would it be possible to build Chimera's version of Python similar to these other versions of Python? Or does the problem lie elsewhere? -- Mark

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Dialog w/ sliders?
by Randy Heiland 21 Apr '08

21 Apr '08

I was wondering if there's a dialog in the gui code that has built-in sliders? E.g., currently our extension module subclasses ModelessDialog; however, our input panel has so many values that it would be convenient if it was embedded in a widget such that sliders appeared when it was resized smaller. thanks, Randy

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