- Chimera-users - RBVI Mailing Lists

saving a stereo image
by Elaine Meng 09 May '08

09 May '08

On May 9, 2008, at 9:04 AM, Pallan, Pradeep S wrote: > > Hi Elaine, > I am trying to save a generate a stereo image by following the > instructions: > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ > frameimages.html > > I captured left eye and right eye images separately, pasted > them side by side ~65 mm apart, and I see this do not appear as > stereo. Any comments and instructions? I can send you the image > if you want to take a look at it. > > Thank you very much, > Pradeep Pallan Hi Pradeep, I think you are looking at old documentation. I don't think the current documentation says anything about saving separate images for left eye and right eye. This is the current page: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/ print.html#stereo Here is the blurb from that page, but it is probably better to go to the URL because there are helpful hyperlinks: Stereo. Wall-eye, cross-eye, and red-cyan stereo images can be saved by changing the graphics window to the corresponding camera mode with the Camera tool (or the command stereo) and using the "same as screen" Image camera mode in the Save Image dialog. Another way to save cross-eye stereo images is with the "stereo pair" Image camera mode; in that case, it does not matter what camera mode is being used in the graphics window, but the resulting image will be twice as wide as the specified size. Those approaches should work, assuming you also have a recent version of Chimera! (last production release Nov 2007 or newer) 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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Selected residues already shown on the screen
by Ibrahim Moustafa 08 May '08

08 May '08

Dear Chimera team, How to include residues previously selected and shown on the screen with a new selection? For example, I did a selection for few residues and displayed them on the screen; then removed the selection. I wanted to run hbond on those residues already on display. How to do that? Thanks, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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MemoryError restoring session
by Eric Pettersen 07 May '08

07 May '08

Christian Rickert wrote: > At the university, I saved a huge project of mine containing a > density map and multiple (!) rigid-body fitted pdbs. > Although this system is a 32-bit Kubuntu 8.04 only (4 Gig of RAM > installed), I observed the same problems with my 64-bit SUSE 10.3 > (4 Gig of RAM installed as well) at work. > > Creating this project took me two days in total, so I really would > appreciate any suggestions from you ... Hi Christian, It's possible that your shell is imposing a limit on memory use by a single process. Before starting Chimera, remove the memory limit of your shell by typing: csh-type shell: unlimit sh-type shell: ulimit -v unlimited Let me know if this helps or not. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to use hbonds spec
by Miguel Ortiz-Lombardía 07 May '08

07 May '08

Hello, I'm trying to follow hydrogen bonds in a trajectory from amber. To do so, I would like to run a 'per frame' script with something like: hbonds spec :100 selRestrict cross relax false However, this fails because apparently no atoms are selected. This fails as well: hbonds spec #0:100 selRestrict cross relax false I can only see the hydrogen bonds if insert a select :100 before the hbonds command. I wouldn't like to see the green 'aura' of the selection, that's why I would like to make the selection within the hbonds command. I'm probably missing something, but cannot figure out what. 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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Tile structure request
by Eduardo Sanz-Garcia 06 May '08

06 May '08

I noticed that the tile structure option arranges the models logically when there are 5 or less models opened. When there are 6 or more, the arrangement is a little bit chaotic, the models are not placed sequentially. Could this option be improved so the sequence is more logical? Thank you very much. Chimera is great!! PS: I am used to work with EM models, I don't know if the previously described behaviour also applies to atomic coordinates models.

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solvent-accessible surface area
by Elaine Meng 06 May '08

06 May '08

Dear Jose, Prof. Ferrin forwarded your question to me. Our program Chimera, the successor to MidasPlus, can calculate the solvent-accessible surface area. It is available for download for Windows, Mac OSX, Linux and other platforms. The features I will mention are relatively new, so you would need to get a recent version such as the May 1 snapshot: http://www.cgl.ucsf.edu/chimera/download.html#snapshots You would first load the structure in Chimera (File... Open for a local file, File... Fetch by ID to get it directly from the PDB). Then there are a couple of different approaches you could take. (1) simply show a molecular surface in Chimera (Actions... Surface... show) or command "surface". The total will be reported in the Reply Log (under Favorites in the menu). You can use the solvent- accessible value or solvent-excluded as you prefer. The difference is explained here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ representation.html#surfaces Besides the total, the values per atom and per residue are assigned as "attributes" named areaSAS and areaSES for solvent-accessible and solvent-excluded, respectively. You can see a histogram of the values by opening "Render by Attribute" (under Tools... Depiction), and you can write out the values to a file by choosing File... Save Attributes from that dialog's menu. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#render The Render dialog can be set to show the values for "atoms" or "residues" (simply the sum over the atoms in each residue). What it writes out are the atom (or residue) specifiers and the value for each, not a grid. (2) instead of doing the calculation in Chimera, you can send the coordinates to a web server with the tool "Area/Volume from Web" (under Tools... Surface/Binding Analysis). There are various options for what you want to calculate. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html Again you get the values assigned as attributes (but this time atoms only) and can view and save them in the same way as described for #1 above. The help links above are part of the User's Guide, which is also accessible from the Help menu of Chimera, once you have downloaded it (Help... User's Guide, Search Documentation, Tutorials). If you still have trouble you can send questions to chimera-users(a)cgl.ucsf.edu 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 May 5, 2008, at 4:52 PM, Tom Ferrin wrote: > ------- Forwarded Message > > Date: Wed, 30 Apr 2008 17:20:27 -0400 > From: Jose Gascon <jose.gascon(a)uconn.edu> > To: tef(a)cgl.ucsf.edu > Subject: midasplus > > Dear Prof. Ferrin > > I am an Assistant Professor in the Chemistry Department at UConn, I am > interested in calculating the solvent accessible area of a protein. I > looked up on the internet and found that the program midasplus is > suppose to do that. The links seem to be outdated and I was not been > able to find the program. I assume that midasplus has probably evolved > to other programs such as chimera. I understand that you were involved > in the development of this program. > > At the end, given a pdb input file, I am just interested in > obtaining a > grid of x,y,z coordinates representing the SAS. > Do you know if there is such a program? Is DMS, from midasplus, still > available somewhere? > > Thanks for your help. > > Sincerely, > > Jose A. Gascon > > > -- > Jose A. Gascon - Assistant Professor > 55 North Eagleville Rd. > Department of Chemistry > University of Connecticut - (860) 486-0591 > Storrs, CT 06269 > http://gascon.chem.uconn.edu > > ------- End of Forwarded Message >

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movie trajectory
by Jean-Paul Armache 05 May '08

05 May '08

Hi Elaine, Eric, Thanks for the answer - I know the webpage for the movies, but it will be helpful to use the savepos command. I will let you know whether this produces the desired effect or further help will be needed. Best regards, Jean-Paul

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movie trajectory
by Jean-Paul Armache 05 May '08

05 May '08

hi all, i have a small question. would any of you know a way to set up a specific trajectory for a camera to move around the molecule? i know you can rotate the whole molecule, but the question is more related to similarity to 3ds max or maya - if you could set up a specific way the camera moves around the molecule (rotation, movement at specific point, zoom, stop, restart, further movement etc) ? maybe the question is trivial, however i haven't found a way to do it (an easy way - you can do quite a huge script with small movements - one step at a time). my question is more about path drawing and setting stop points. regards, jean-paul

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Re: [Chimera-users] transparent surfaces (fwd)
by Greg Couch 05 May '08

05 May '08

Just so everyone on the list knows. Extrapolating from what Charles said, the error was probably that MegaPOV wasn't able to include the transforms.inc file because MegaPOV wasn't configured properly to include the POV-Ray library files. And on Mac OS X, Linux, and other UNIX systems, to use the CHIMERA/bin/povray.exe program outside of chimera, you need to setup the shared library path to include CHIMERA/lib. Chimera does that setup automatically for many of the programs in CHIMERA/bin, so we should probably fix it for povray as well, but if you're going to use your own POV-Ray anyway, like the multi-threaded 3.7 beta release, then that is not an issue. - Greg ---------- Forwarded message ---------- I figured it out. In MegaPOV you need to set the library path for the render, also POVray 3.6 will not work as a standalone application in Mac OS 10.4 and higher. Charles On May 5, 2008, at 2:15 PM, Greg Couch wrote: > On Thu, 1 May 2008, Charles Midgett wrote: > >> 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 > > That is news to us. The chimera povray output was only tested with the > POV-Ray 3.6.1 renderer that comes with chimera. Please submit a bug report > using chimera's Help / Report a Bug dialog and include the name and version > number of the other POV-ray renderers, as well as the error message you get. > > Thank you, > > Greg Couch > UCSF Computer Graphics Lab

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Consistency of surface color
by Bui Khanh Huy 05 May '08

05 May '08

Hi all, I have a problem with color consistency on Chimera. The surface color of my model from my Windows server is different than that from my linux server. Even when I connect from home to the linux server, the color render is also different from those two above. I use the same session for all of them but the color comes out quite different on different machines. Is there anyway to avoid this inconsistency? Regards, Huy

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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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