- Chimera-users - RBVI Mailing Lists

surface rendering
by Peter Lewis 22 Jul '08

22 Jul '08

Dear Chimera-Users I've recently changed my computer to a quad core system which runs Red Hat and virtual Windows. I've installed chimera (32 bit) on both linux and windows. I have tried using chimera downloads posted in both June and July this year but cannot get surface rendering to work for either operating system. Is this a bug with recent versions of chimera, and if so, how do I fix it, or is it a bug with my new system? Any help gratefully appreciated. Peter A/Prof Peter Lewis Molecular Microbiology Group School of Environmental and Life Sciences University of Newcastle Callaghan NSW 2308 Australia Ph: +612 4921 5701 Fx: +612 4921 5472

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Movie contains overlapping windows
by Tom Goddard 21 Jul '08

21 Jul '08

Hi Jean-Paul, Yes movie recording will include windows that overlap the Chimera graphics window. This is an unfortunate limitation of the Chimera image saving caused by it capturing images directly from the screen. On some platforms an overlapped window may not appear because the contents of the graphics window are saved even when another window overlaps. But that is not the case on most platforms. So in most cases the machine cannot be used for other purposes when a movie rendering is in progress. We have been interested in eliminating this limitation for some years but Greg Couch who handles image capture has not had time to get to it, If you use raytracing for the movie capture then it does not matter if the Chimera window is covered. But raytracing takes much longer to render. Tom Jean-Paul Armache wrote: > Hello again, > > I re-checked the spider loading, and now it seems to work. I don't > know why it did not previously. > > I have another question though. I have two versions of Chimera on my > computer now. I am using Chimera X Window to generate movies, > because in respect to the Aqua version, if I start another application > (like Keynote, web browser etc), the movie does not contain any parts of > the screen on top of it. > If I use the Aqua version (and on Linux is the same), it includes the > currently on-top graphics into the movie. Is there a way to not do so in > Aqua? > > Best regards, > > Jean-Paul Armache >

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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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Possible image saving bug
by Elaine Meng 17 Jul '08

17 Jul '08

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

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Possible image saving bug
by Walter Novak 17 Jul '08

17 Jul '08

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. Also, when using pov-ray, the balls are completely devoid of shininess, regardless of my shininess settings (I set it to 128). That is the last image. Thanks, Wally 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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Coloring a binding site
by Tom Goddard 16 Jul '08

16 Jul '08

Hi Andy, To color a binding site I would select the ligand (DNA in your case) then select all the nearby atoms using Select / Zone..., then use Actions / Color to color those atoms. Tom Anindito Sen wrote: > Another question - I need to color a portion of the crystal structure > differently (ribbon diagram) in order to indicate the binding sites of > the DNA with the protein molecule and how do I do that. > > Thanks and Best Wishes > Andy

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possible bug
by Ben Keshet 16 Jul '08

16 Jul '08

Hi, when I un-select atoms, I had some weird long lines crossing my structures across (picture attached). I restarted the program how ever the same exact thing happened again. The two files that were opened worked perfectly in the past and before I un-selected the atom (ctrl+left click in the "air"). Other wise - great software. Thank you. Ben

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Re: [Chimera-users] History feature for command line between sessions
by Eric Pettersen 15 Jul '08

15 Jul '08

> On Apr 17, 2008, at 8:52 AM, Boaz Shaanan wrote: > > > The history of commands in the command line mode is retained > > within a session and is very convenient but I was wondering whether > > there is a feature that will allow you to recall commands from > > previous sessions (such as in O for example - it generates an .o- > > history file which is being constantly updated and is very > > convenient). If not, is it possible to request the addition of such > > a feature ? There are many ways to implement this of course and I'm > > sure you'll find the best way, if it's not already there lurking in > > Chimera. > > Hi Boaz, > Good idea -- and shouldn't be too hard to implement. I was thinking > of remembering the last 100 commands. Will that be enough you think? > > --Eric This is implemented now. It should show up in the next daily build that works. Only remembers 60 by default, but that number is changeable in Preferences. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Can't type in Chimera
by Thomas Goddard 15 Jul '08

15 Jul '08

Hi Andy, I don't know how Chimera could get in a state where it will not accept any typed input. Do you recall the last thing you did in Chimera before it stopped accepting key input? If I were stuck in this situation and could not type a file name to save the Chimera session I would create an empty file with the session file name I wanted using a text editor. Then choose that file with the mouse in the Chimera session saving dialog. Desperate measures. If you can reproduce the problem please tell me how and I will fix Chimera. Tom Anindito Sen wrote: > HI Tom > > I have installed the latest version of Chimera on my LINUX box Fedora > Core 6.0. I faced a strange problem- while carrying out a docking of a > crystal structure in a density map I was using the command line for the > differnt movements and controls. After some time I am unable to type > anything on the command line. Infact I am even unable to save the > session as I cannot type the "NAME" of the session. I checked my keyboad > and typed on the terminal and on text editiors and it worked normally. > > Waiting for your response. > > Best Wishes > Andy > > > Dr. Anindito Sen (Ph.D) > Research Associate , Dept. of Biochemistry and Molecular Genetics > University of Virginia > Box 800733 Charlottesville, VA 22908

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Re: [Chimera-users] reg. ribbon reprsentation
by Elaine Meng 15 Jul '08

15 Jul '08

>> >> Greetings. I have already posted a similar question on the forum >> previously and hence i am writing to your email. My problem is when >> i open a protein pdb, i get wonderful ribbon representation when i >> opt for it. But when i give a protein pdb with only a CA atoms/ >> CA,C,N atoms, i dnt get the ribbon representation. I understand >> that ribbon is constructed by considering CA,C,N,O and OXT atoms. >> What i did was that i simply removed O and OXT atoms by going >> through Tools--> Depiction --> Ribbon style Editor. It may be a >> wrong idea to do that. But i would appreciate if you could write me >> some way to draw the ribbon for protein having only CA or CA,C,N >> atoms IF POSSIBLE. >> >> Regards, >> Bala >> Hi Bala, If you have N-CA-C atoms, it actually works pretty well if you open Ribbon Style Editor, go to the "Residue Class" tab, choose "amino acid" but then change the "Orientation atom" to C instead of O, and Apply. (You still need to show ribbon if you didn't already do that.) You can save and name the new residue class for re-use in some later Chimera session if you want. The resulting ribbon looks the same to me as the standard ribbon made from N,CA,C,O (I tested this by writing a PDB of only the N,CA,C atoms from a complete structure, reading it back in, and experimenting with Ribbon Style Editor). http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbon… If you have CA atoms only, then there is no way to figure out the plane of the ribbon - it does not work to set both the "Guide atom" and "Orientation atom" to CA. Unfortunately this prevents you from displaying "licorice" ribbons even though they don't use an orientation plane. My only solution in this case is to use some program to build the additional atoms from the CA trace, for example this web server: http://www.ebi.ac.uk/Tools/maxsprout/index.html 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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Re: [Chimera-users] email address
by Khanei Mkumeni 14 Jul '08

14 Jul '08

khmlukundo(a)gmail.com

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SpaceNavigator with Linux
by D. Greening 14 Jul '08

14 Jul '08

Hi, I just downloaded Chimera 1.2540 and was pleased to see that the SpaceNavigator 3-D mouse is now supported for Windows and Mac. Will those of us who use Linux be able to use our SpaceNavigators with Chimera any time soon? Thanks. D. Greening Memorial University of Newfoundland

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drawing molecules
by Kathleen.Zocher＠ernaehrung.uni-giessen.de 14 Jul '08

14 Jul '08

Dear Sir or Madam, I`ve just one question concerning some special tools of Chimera. Is it possible to draw small molecules (ligands) within chimera? I can not find some information for this problem in the manual. For further docking experiments I just need a 3D-structure which is minimized (in a mol2 file). Many thanks in advance! Sincerely yours Kathleen Zocher ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Question about bond length modification
by Benjamin G.S. Horsman 14 Jul '08

14 Jul '08

Hello, I have what appears to be simple problem but is I can't find the solution in previous mailing list queries. My problem is that I am unable to modify the lengths of any bonds in a PDB molecule. I am rather frustrated with myself over such a stupid problem, having tried dozens of times over dozens molecules to get it right but to no avail. Any possible solutions from the community? I am using MacpyMol to generate PDB structures and Chimera v1 build 1470. Thanks for any help, Ben

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Re: [Chimera-users] [Chimera-announce] Chimera production release
by Elaine Meng 13 Jul '08

13 Jul '08

Hello Yao, Don't worry, the new versions still include the ability to fit map in map. It is simply that two tools were combined into a new tool with a slightly different name. Changes in this production release relative to the previous one include: "Fit Model in Map" and "Fit Map in Map" (Volume Data) — * merged into new "Fit in Map" tool * can update fit values continuously * can simulate map from atomic coordinates, report map-map correlation current documentation: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/ fitmaps/fitmaps.html 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 On Jul 12, 2008, at 11:49 PM, Yao Cong wrote: > Hello Chimera developer, > > Appreciate your great efforts to make Chimera an perfect tool for > Cryo-EM study. > > I and many of my colleges notice that in your latest versions, you > omit the "fit map into map" module, which is very convenient in > many cases. Is there a specific reason for that? And we all > consider it will be very helpful if you could add this function > back in your next version, maybe daily release? Otherwise, we still > keep the old version to have that function and meanwhile install > your newer version to enjoy the newer functions. > > Thanks, > Yao > ----------------------- > Yao Cong, Ph.D. >

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Creating abridged multimer
by Francesco Pietra 12 Jul '08

12 Jul '08

I am posting again after having once again subscribed In order to create an abridged multimer made of non covalently bound subunits (from available pdb of subunit) which is the preferable route? (1) Load the monomer, delete substructures, and then assemble an abridged multimer? Are the headers furnished with the monomer OK for the abridged subunit? (2) Build the unabridged multimer and proceed to simplify each subunit the same way? Thanks francesco pietra

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