- Chimera-users - RBVI Mailing Lists

10.5 mac Chimera hangs on resize
by Eric Pettersen 21 Jul '08

21 Jul '08

On Jul 21, 2008, at 4:32 PM, Jean-Paul Armache wrote: > Submitter Name: Jean-Paul Armache > Platform: (X11) Darwin 9.4.0 i386 > Chimera Version: production version 1 build 2540 2008/07/09 > Description > well, the X window tends to hang just after manually resizing the > window. Hi Jean-Paul, I was able to reproduce this and was able to come up with two solutions. One is to resize carefully. In particular, do not release the mouse button until you have stopped the mouse. I find that this always avoids the hang. The other solution is to upgrade your X11.app to the 2.3.0 version (as a prerequisite you need to be at OS X 10.5.4. or later). You can download 2.3.0 from here: http://xquartz.macosforge.org/trac/wiki/X112.3.0 --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Problems saving eps files on Windows
by Julianne Chung 21 Jul '08

21 Jul '08

Hi, I am having trouble saving images in Chimera and was hoping that you may be able to help me out. I am running the latest version of Chimera on Windows. I have a molecule that I want to save as an eps file. I got to File --> Save Image --> Save As -->change the file type to eps and click Save, but no eps file appears in the directory I specified. Jpeg, png and tiff all work fine, but I can't get eps and ps to work. I've installed Ghostscript too, but that doesn't seem to help. Any suggestions are appreciated, Thanks, Julianne Chung Emory University

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Re: [Chimera-users] Possible image saving bug
by Walter Novak 21 Jul '08

21 Jul '08

Hi Elaine, I agree that some colors are shinier than others. Also, my brightness was not zero, but was the default of 1. I think however, I have tracked the issue down to the position of my lights. I had them pretty straight on and resetting this position gives the pov-ray shininess I was expecting. Thank you, Wally On Jul 17, 2008, at 9:29 PM, Elaine Meng wrote: > Hi Wally, > on to problem #2. > > I was unable to reproduce this problem. Are you sure that the > "brightness" is >0? If brightness is zero, there are no > highlights. Below are two images, the top with shininess 128 and > brightness 10, the bottom with shininess 128 and brightness 0. > Actually now that I look at it carefully, the bottom one confuses me > because the cyan things are still shiny, so I'm cc-ing the others > (Greg, any explanation??). The other colors in the bottom image are > non-shiny as expected, however! > > Best, > Elaine > > <imagebright10.png> > > > <imagebright0.png> > > > Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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<< two questions about Chimera >>
by Hatuey Hack 21 Jul '08

21 Jul '08

Hi all, I have to questions about Chimera: 1st.- Is it possible to search the mailing list to avoid doing questions that were already answered? 2nd.- As I do not know the answer to the first question, I would like to know how I can visualize double and triple bound as well as aromatic rings explicitly within Chimera. Regards, Hatuey

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Morphing aligned maps
by Tom Goddard 21 Jul '08

21 Jul '08

Hi Haixin, The morph map tool just linearly interpolates the two volume 3-d arrays at each grid point. So it does not work correctly if you have moved one map relative to the other since it ignores their relative positioning. To use it in this case you need both maps to use the same grid so you have to "resample" one map. That is you recompute that map on the same grid as the other map using interpolation. The command to do that is "vop", for example, vop #1 resample onGrid #0 modelId #2 Now use morph map between model #0 and the resampled volume #2. Morph map doesn't provide a way to morph between more than 2 maps. That would be useful. You can use it to morph the separate pairs of maps 0 -> 1, then 1 -> 2. You can almost record a movie of this using the following trick. First record 0 -> 1 but when it asks you to save the movie leave that dialog alone (don't cancel since that will erase the saved image frames). Then record 1 -> 2 and then save the movie. Frames from both morphs will be included in the movie. The problem is that each morph plays both forward and backward so you get 0 ->1 -> 0 jumps to 1 -> 2 -> 1. You could avoid the looping with a small modification to the Morph Map code. You would edit chimera/share/MorphMap/gui.py adding a few lines in the next_frame_cb() routine. if next_f >= fmax: next_f = fmax self.step_direction = -1 would become if next_f >= fmax: next_f = fmax self.step_direction = -1 if self.recording: self.finish_recording() Keep indentation as shown since that is important in Chimera. Tom Haixin Sui wrote: > Hi, Tom > > ... > I have a map morphing question. I manually aligned two maps in Chimera > in order to do a map morphing for my presentation. However, the map > morphing does not happen at the aligned positions but shifted the > second map back to the position before the alignment. I wonder how > should I get arroudn this problem. Saving the second maps relatie to > the first and read it in again? > > Meanwhile, I have several maps I want to do map morphing and show > changing in between them. It will be great if chimera can work with > more than one maps and show the changed from map#1 to map#2, and then > #3 ... This feature can be helpful when people want to show several > conformational changes. > > Haixin

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selection of a specific region from different chains
by Tom Goddard 21 Jul '08

21 Jul '08

Hi Andy, Use a command like "select :100-200 to select residues 100 through 200 in all chains. Tom Anindito Sen wrote: > HI Tom > I have a 5 separate chains (of the same crystal structure) docked > along my filament reconstruction. How do I select and highlight a > certain length of amino acids from each and every chain. Problem > happens when I try to select a region of the second or 3rd chain, > which "deselects" the pervious selection. > > Best Andy

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3 volume histograms
by Tom Goddard 18 Jul '08

18 Jul '08

Hi Haixin, Chimera can display any number of volume data sets. But it only shows 3 histograms in the volume dialog, the 3 whose settings were most recently changed. You can use the Data menu on the volume dialog to show the histogram for a different volume (replacing the least recently used of the current 3 histograms). If you want a different maximum number of histograms (like 1 or 5) there is a setting in the volume dialog Data Display Options panel for "Maximum number of histograms". To make this new value the default use the Features menu Save Default Dialog Settings. Tom > >> *From: *Haixin Sui >> *Date: *July 17, 2008 6:12:29 PM PDT >> >> Installed the newest version and found a problem. This version can >> only work with at most three density maps. When you have four or more >> density maps read in, the volume viewer window will only display the >> control for the last three maps. >>

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Distance between atoms using Python
by Tom Goddard 18 Jul '08

18 Jul '08

Hi Ed, Attached is some Python code for controlling ligand display based on distance between two atoms. Tom Edward Brignole wrote: > > Tom, > > Thanks again for your help with that atom display. Got another > MDtrajectory issue for you. I've got a ligand in each of 10 domains > in the structure and I only want to display the ligands in the frames > that have less than a certain distance between a particular atom in > the ligand and a particular atom in a neighboring domain. > > The distance command won't work for me because all it does is add a > distance to the distance dialog when I need it as a variable in the > script to evaluate with "if distance < 10: display atomspecs" > > Sorry to keep bugging you with these things but I assure you it isn't > without trying for several hours to no avail before finally resorting > to asking. > > Ed > def atom_distance(spec1, spec2): from chimera.specifier import evalSpec atom1 = evalSpec(spec1).atoms()[0] atom2 = evalSpec(spec2).atoms()[0] d = atom1.xformCoord().distance(atom2.xformCoord()) return d from chimera import runCommand if atom_distance('#0:15.B@C4', '#0:7.A@N3') >= 10: runCommand('display #0:SPM') else: runCommand('~display #0:SPM')

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center of mass for multiple models.
by Jean Didier Pie Marechal 18 Jul '08

18 Jul '08

Hi everyone, I am stuck with a script and my mistake seems to come from my poor understanding on how to treat atom coordinates with multiple models. I join to this e-mail a chimera file with a simple system to illustrate my problem. In the file, I have two indentique phenyl moleculer each of them in different models and I would like to stock the center of mass of both molecules in a list. I wrote this very simple script using the way of calcuting the center of mass you provided me recently. import chimera import BuildStructure from chimera import runCommand as run from chimera import selection, Vector from chimera import openModels, Molecule, Point #Stock the two fragments in the list FRAG run("select") frag=[] for i in chimera.selection.currentResidues(): frag.append(i) #Calculate center of mass of both entities #stocked in the list MAS mas=[] for i in range(len(frag)): sum=0 center = Vector(0, 0, 0) for a in frag[i].atoms: sum += a.element.mass center += a.element.mass * Vector(*a.coord().data()) mas.append(Point(center[0]/sum,center[1]/sum,center[2]/sum)) print i,mas[i] The results I have are 0 20.0465 70.3735 23.9063 1 20.0465 70.3735 23.9064 Basically, the coordinates of the center of mass are the same? What did I do wrong in the way I treated this problem? Thanks a lot for any answer, All the best JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dijous, Juliol 17, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 63, Issue 17 > 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: Possible image saving bug (Greg Couch) > 2. Possible image saving bug (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 17 Jul 2008 10:35:26 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Possible image saving bug > To: Walter Novak <wnovak(a)brandeis.edu> > Cc: Chimera forum <chimera-users(a)cgl.ucsf.edu> > Message-ID: <Pine.OSF.4.63.0807171001010.1939086(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Thu, 17 Jul 2008, Walter Novak wrote: > > > Hi All, > > > > I submitted a bug report on this, but the behavior is both odd > and > > reproducible for me. Using the latest production release and > trying to save > > an image using supersampling, the image is not stitched back > together > > appropriately. It is odd, because it always happens for a certain > session > > file I have. It doesn't seem to happen if I open a new molecule > and make a > > picture. I can provide the session file if needed. First image is > using 3x3 > > and second is 6x6. > > I see from the bug report that you're using Mac OS X 10.5. We are > having > "issues" with the new X11 application in 10.5. And we have seen > that > slightly different X11 applications are installed on otherwise > identical > Macs and that reinstalling from the Mac OS X Install Disk fixed a > non-chimera bug. > > Also, I have read on the web that if you install the 10.4 X11 > application > on 10.5, then OpenGL applications will work better. Since that is > not an > option for everyone, we are spending more time to improve the Aqua > version > that is available as a Snapshot release on the chimera download > page. It > has different bugs, but the graphics is better. So you should try > it out > and see how well it works for you. > > Greg Couch > UCSF Computer Graphics Lab > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Jul 2008 10:40:13 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: [Chimera-users] Possible image saving bug > To: wnovak(a)brandeis.edu > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <B15630DD-299C-4B48-A8B4-469FA8995872(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Wally, > I also had this tiling problem. We think it may be something about > > X11 in Mac OS 10.5 (possibly just 10.5.4), as the problem has not > been > observed with 10.4/X11. > > Two workarounds that were successful in my case (I don't know if > they > will fix all instances of the problem): > > (A) simply show the Command Line before saving the image. I tried > hiding it again after that, but then the problem reoccurred, albeit > in > a more subtle fashion. > > (B) save the session, restore it in the aqua version of Chimera > (still > on Mac OS 10.5.4 but not using X11) and save the image. Yeah, (A) > is > easier, but I didn't discover that one until this morning, after > receiving your mail. > > I hope these solutions are general! Sorry about the inconvenience, > 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 > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 63, Issue 17 > ********************************************* >

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center of mass for multiple models
by Jean Didier Pie Marechal 18 Jul '08

18 Jul '08

Hi everyone, I am stuck with a script and my mistake seems to come from my poor understanding on how to treat atom coordinates with multiple models. I join to this e-mail a chimera file with a simple system to illustrate my problem. In the file, I have two indentique phenyl moleculer each of them in different models and I would like to stock the center of mass of both molecules in a list. I wrote this very simple script using the way of calcuting the center of mass you provided me recently. import chimera import BuildStructure from chimera import runCommand as run from chimera import selection, Vector from chimera import openModels, Molecule, Point #Stock the two fragments in the list FRAG run("select") frag=[] for i in chimera.selection.currentResidues(): frag.append(i) #Calculate center of mass of both entities #stocked in the list MAS mas=[] for i in range(len(frag)): sum=0 center = Vector(0, 0, 0) for a in frag[i].atoms: sum += a.element.mass center += a.element.mass * Vector(*a.coord().data()) mas.append(Point(center[0]/sum,center[1]/sum,center[2]/sum)) print i,mas[i] The results I have are 0 20.0465 70.3735 23.9063 1 20.0465 70.3735 23.9064 Basically, the coordinates of the center of mass are the same? What did I do wrong in the way I treated this problem? Thanks a lot for any answer, All the best JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dijous, Juliol 17, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 63, Issue 17 > 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: Possible image saving bug (Greg Couch) > 2. Possible image saving bug (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 17 Jul 2008 10:35:26 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Possible image saving bug > To: Walter Novak <wnovak(a)brandeis.edu> > Cc: Chimera forum <chimera-users(a)cgl.ucsf.edu> > Message-ID: <Pine.OSF.4.63.0807171001010.1939086(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Thu, 17 Jul 2008, Walter Novak wrote: > > > Hi All, > > > > I submitted a bug report on this, but the behavior is both odd > and > > reproducible for me. Using the latest production release and > trying to save > > an image using supersampling, the image is not stitched back > together > > appropriately. It is odd, because it always happens for a certain > session > > file I have. It doesn't seem to happen if I open a new molecule > and make a > > picture. I can provide the session file if needed. First image is > using 3x3 > > and second is 6x6. > > I see from the bug report that you're using Mac OS X 10.5. We are > having > "issues" with the new X11 application in 10.5. And we have seen > that > slightly different X11 applications are installed on otherwise > identical > Macs and that reinstalling from the Mac OS X Install Disk fixed a > non-chimera bug. > > Also, I have read on the web that if you install the 10.4 X11 > application > on 10.5, then OpenGL applications will work better. Since that is > not an > option for everyone, we are spending more time to improve the Aqua > version > that is available as a Snapshot release on the chimera download > page. It > has different bugs, but the graphics is better. So you should try > it out > and see how well it works for you. > > Greg Couch > UCSF Computer Graphics Lab > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Jul 2008 10:40:13 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: [Chimera-users] Possible image saving bug > To: wnovak(a)brandeis.edu > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <B15630DD-299C-4B48-A8B4-469FA8995872(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Wally, > I also had this tiling problem. We think it may be something about > > X11 in Mac OS 10.5 (possibly just 10.5.4), as the problem has not > been > observed with 10.4/X11. > > Two workarounds that were successful in my case (I don't know if > they > will fix all instances of the problem): > > (A) simply show the Command Line before saving the image. I tried > hiding it again after that, but then the problem reoccurred, albeit > in > a more subtle fashion. > > (B) save the session, restore it in the aqua version of Chimera > (still > on Mac OS 10.5.4 but not using X11) and save the image. Yeah, (A) > is > easier, but I didn't discover that one until this morning, after > receiving your mail. > > I hope these solutions are general! Sorry about the inconvenience, > 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 > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 63, Issue 17 > ********************************************* >

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