- Chimera-users - RBVI Mailing Lists

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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