- Chimera-users - RBVI Mailing Lists

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 �� 30 Apr '08

30 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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