- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] reading in hdf5 files in chimera
by Joshua Turner 08 Sep '08

08 Sep '08

Hi, I have created a 3D hdf5 file and am having trouble displaying it in Chimera. Is there something specific chimera looks for that it needs to read in the .h5 file, to be able to display the file? Thanks, Josh

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SGI build going the way of the dodo
by Eric Pettersen 04 Sep '08

04 Sep '08

We are decommissioning our SGI machines as of September 15th, which means that the 1.2540 release was the last production release for SGI and that daily builds will stop on the 14th or 15th (those final builds will remain available on the Daily Builds page for a few months at least). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] aqua version of Chimera
by Elaine Meng 03 Sep '08

03 Sep '08

On Sep 3, 2008, at 12:08 PM, Anindito Sen wrote: > Hi Eline > The aqua version of Chimera when installed on my Macbook(memory > 4GB, proc. 2.2 Core 2 Duo) seems to come up with a strange problem > of flickering of the main display window each time I move another > window or alter the position of a crystal structure. However I have > not faced anything on the MacOSX (X windows)version. I was > wondering what possibly can be the reason and that if ony one else > in the community have faced similar problem of this type. > Best > Andy > > Dr. Anindito Sen (Ph.D) > Research Associate , Dept. of Biochemistry and Molecular Genetics > University of Virginia > Box 800733 Charlottesville, VA 22908 Hi Andy, This behavior in Aqua Chimera is intentional, allowing a window to become active immediately instead of requiring an extra click when you move the cursor into that window. However, if you would rather have extra clicking than the flickering, you can turn it off in recent versions of Chimera (within the last month): open Preferences (under Favorites), change to "Mouse" category, set "Window focus follows mouse" to false. This preference only appears in the Mac Aqua version. I would like to remind everybody: To ask questions, please email chimera-users(a)cgl.ucsf.edu (unless something confidential is included), and to report problems, please use "Help... Report a Bug" or email chimera-bugs(a)cgl.ucsf.edu . It is better to send to these e-mail addresses than to an individual, because that person might be on vacation or unavailable at the time and you might not get an answer. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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] sulfone files
by Eric Pettersen 03 Sep '08

03 Sep '08

Hi Barb, There are two issues here. One was that though the heavy-atom positions were identical, the added hydrogens weren't positioned identically because of "steric clashes" between the two molecules when placing hydrogens (this was in some fairly newly-added code). I modified the new code to ignore clashes between sibling submodels (other analogous older code was already doing this). With the modified code and with the two PDB files merged so that the molecules open into model 0.1 and 0.2, the hydrogens get added identically. The other issue is that antechamber only determines charges to somewhere around 0.01 accuracy, even with the atoms at identical positions. Now, Chimera is supplying antechamber with identical positions, but giving them in a different order between the two residues, so that the resulting output isn't identical. I've modified the add-charge code so that it will now present the atoms in the same order as they were input -- so the result is that the charges vary only minimally now. Nonetheless, they shouldn't really be perceived as more accurate than about +/-0.01 charge units. You'd probably have to ask on the Amber mailing list why this is so and if there is anything that can be done or will be done about it. These changes will be available in tonight's daily build, which you could get tomorrow from www.cgl.ucsf.edu/chimera -- follow the "Daily Builds" link. --Eric On Sep 3, 2008, at 6:17 AM, Barb Truitt wrote: > Eric - Thank you for your help. I find the Chimera list incredibly > helpful. > I've verified that the pdb files have the same coordinates. I also > redid the DOCK PREP without any rotation of either molecule and > still have different charge assignments. Here are the four files. > The carbons that vary the most between the two are the ones in the > aromatic ring with a single methoxy group and the ones near the > chlorine. I'm also sending an Excel file where I've sorted the atoms > based on their coordinates so that I could check the assigned > charges. I've color-coded the carbons that vary significantly. > > Barb > <charge > comparison > .xls > > > < > SSR149415 > .pdb><SSR149415_SR4.pdb><SSR149415_SR_T.mol2><SSR149415_T.mol2>

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problem with chimera
by Jean-Paul Armache 03 Sep '08

03 Sep '08

Hello, Due to some long needed changes, I have switched to CentOS 5.2. Everything was fine for some time, but then, when trying to run Chimera, I encountered the following error (applies to all versions of Chimera on my harddrive - 1.2470, 1.2492 and 1.2540): Traceback (most recent call last): File "/opt/chimera/chimera1.2492/share/__main__.py", line 65, in ? value = chimeraInit.init(sys.argv) File "/opt/chimera/chimera1.2492/share/chimeraInit.py", line 302, in init splash.create() File "/opt/chimera/chimera1.2492/share/chimera/splash.py", line 17, in create splash = Tk.Frame(root, background="white") File "/opt/chimera/chimera1.2492/lib/python2.4/lib-tk/Tkinter.py", line 2375, in __init__ Widget.__init__(self, master, 'frame', cnf, {}, extra) File "/opt/chimera/chimera1.2492/lib/python2.4/lib-tk/Tkinter.py", line 1862, in __init__ self.tk.call( _tkinter.TclError: unknown color name "white" I have tkinter installed, python running properly, everything functional. Except for that. Do you know what could be done to fix it? Best, Jean-Paul

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v. 2540 linux - core dump (?!?!?!)
by Boaz Shaanan 02 Sep '08

02 Sep '08

Hi, After installing v. 2540 for linux I get 'floating exception' and core dump. The installation went fine as far as I can tell. It's a laptop running Mandrake 10. So far, I've had no problem running chimera on it. any clue about what might have gone wrong ? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Chimera running un der 64 bit Vista
by Charles Letner, Ph.D. 02 Sep '08

02 Sep '08

Hello all, Does Chimera run under 64 bit Vista? Thinking about a new desktop and sure would like to go 64 bit. Cheers, Chuck Charles Letner, Ph.D. Alpharetta, GA 30004

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Display
by James Fethiere 02 Sep '08

02 Sep '08

Hi, I have a sudden problem with the display in version 1.2509. I was working with a session with about 20 models opened. For whatever reason, I just can't display any on the screen anymore; even if all are selected in the model panel. Am I missing something or is this a bug? Thanks James

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assignment of charges
by Barb Truitt 02 Sep '08

02 Sep '08

I have two different pdb files that differ only in how the atoms are listed in the atom name columns. In one file all of the Carbon atoms are listed simply as C. In the other file, the carbon atoms are numbered C1, C2, etc. This is true for the other atoms in the molecule, which is not a peptide chain. The mol2 files created by Chimera under the dock prep procedure have different charges assigned to the atoms, differing most in the aromatic carbons. Some of the hydrogens also have different charges assigned to them. Most of the differences are small, but some are 10%. What is the explanation for this? Barb Truitt

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sulfone
by Barb Truitt 02 Sep '08

02 Sep '08

I am trying to assign charges to a compound that contains a sulfone group. The charge assignment depends upon how I name the atoms. The atom assignment for the oxygens that are part of the sulfone group and the sulfur itself vary depending upon how they are named. How should I name them so that they are handled correctly? Barb Truitt PS - I receive the Chimera list emails, but my outgoing email address apparently doesn't match the one that I used to sign up for the list. Is there a way to fix that?

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POV-ray ignoring surface clipping
by Monica Tello 02 Sep '08

02 Sep '08

Help! I am having trouble saving my images when they have a surface clipped to show the inside. I attach an example for clarity, where the same view was saved with/without POV ray.. If I have a surface around my ligand and is partially clipped, at the time of saving the image: - If I save it without using POV-ray, it saves the exact same view as on the screen, with the surface clipped. - If I use POV-ray, it saves it with the full surface around the ligand, ignoring the clipping I had done. I have tried modifying several POV-ray settings but nothing has worked! Have you got any suggestions? Thanks! Monica SURFACE CLIPPED WITH POV-RAY, SURFACE DOES NOT SHOW THE CLIPPING! ------------------------------------------------- Monica Tello Soto, PhD The Salk Institute for Biological Studies Chemical Biology and Proteomics 10010 North Torrey Pines Road San Diego CA92037 858 453 4100 x1946 tello(a)salk.edu ------------------------------------------------

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POV-ray ignoring surface clipping
by Monica Tello 02 Sep '08

02 Sep '08

Dear all, I am trying to save a Figure that shows my ligand with its surface around partly clipped, and use POV Ray. The problem is that POV Ray modifies the output of the figure: the final picture shows the full surface around the ligand, although on the screen I designed it so that you can see the surface partially clipped. If I use transparency on the surface, POV Ray also ignores this and shows still the full surface around the ligand, and opaque. If I don´t use POV Ray, then I get the figure as seen on the screen! Why is POV Ray ignoring the surface as I want it? It ignores any kind of alteration of the surface! I was using the default POX Ray settings, although by now I have tried to change some of the ones I thought may be related to this, based on the Chimera Manual, but I haven´t had any success. Can anyone help me with this? It will be very much appreciated! I include an example of the same figure saved with and without using POV Ray. The one without using POV ray is the one that looks like what I designed on the screen. Thank you very much!! Monica ----------- ------------------------------------------------- Monica Tello Soto, PhD The Salk Institute for Biological Studies Chemical Biology and Proteomics 10010 North Torrey Pines Road San Diego CA92037 858 453 4100 x1946 tello(a)salk.edu ------------------------------------------------

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Re: [Chimera-users] ESP surface, DelphiController
by Elaine Meng 02 Sep '08

02 Sep '08

On Sep 1, 2008, at 9:14 AM, James Fethiere wrote: > > Once the .dx file is loaded in Chimera, I get a nice ESP map. > However, it seems sensitive!! how? well, when I color the surface > of a transcription factor bound to DNA (1DH3) according to the dx > ESP loaded file, it's nice. But when I display the ribbons of the > bound DNA in the same model and color these ribbons, the previous > surface reverts to the default Chimera colors and I loose the ESP > from the dx file. Quite strange no? Hi James, The reason is that the surface cannot have "custom" colors (e.g. ESP coloring) and coloring to match the underlying atoms at the same time, even in different areas of the surface. If you make sure to color only ribbon and not surface, the surface should stay ESP-colored. If you are using the Actions... Color menu, make sure to check only "ribbons" as what will be colored, color the ribbons, and then change it back to the default "all of the above" coloring targets. If you are using a command, then something like color red,r :30-50 specifies coloring ribbons only (the ",r" part). The alternative is to do all the ribbon/atom coloring first, ESP-color the surface last. > > It is also not possible to select this dx ESP file in a command > file to make a movie. And if it is displayed before movie record > starts, I get a black frame movie with the avi encoding (yes I did > modify the video acceleration in media player). So I guess it will > be still pictures. Check out the session attached. > What are you trying to do with the surface in this movie (why are you trying to select or specify it?). Most command-line selections are based on specifying a set of atoms, so you would just specify the atoms associated with the molecular surface. However, I would need to know which commands you are trying to use to be more specific/ concrete, or let you know if what you want to do is possible with commands. > Thanks > > James I am unable to deal with that attached session because it is just shown as a zillion lines of text beneath the mail message. My cut- paste attempts failed. You could instead use Help... Report a Bug and attach the session to it to illustrate the black movie problem. We may or may not be able to reproduce it, but having the session (and perhaps also your movie script?) would help. It may only let you attach one thing, so I'd say attach the session and put the script (or some short version that exhibits the problem) as part of the message text. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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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POV-ray ignoring surface clipping
by Monica Tello 31 Aug '08

31 Aug '08

I am having trouble saving my images when they have a surface clipped to show the inside. If I have a surface around my ligand and is partially clipped, at the time of saving the image: - If I save it without using POV-ray, it saves the exact same view as on the screen, with the surface clipped. - If I use POV-ray, it saves it with the full surface around the ligand, ignoring the clipping I had done. I have tried modifying several POV-ray settings but nothing has worked! Have you got any suggestions? Thanks! Monica ------------------------------------------------- Monica Tello Soto, PhD The Salk Institute for Biological Studies Chemical Biology and Proteomics 10010 North Torrey Pines Road San Diego CA92037 858 453 4100 x1946 tello(a)salk.edu ------------------------------------------------

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automating/scripting bond rotation
by E. Merkley 29 Aug '08

29 Aug '08

Hello chimera team, I am trying to evaluate which regions of (chi1,chi2) space for a particular tryptophan residue create steric clashes with a bound ligand. I see from the archives that findclash can be called from the command line, but I have been unable to find a way to use the "adjust torsions" feature from the command line. Is this possible? If not, any other suggestions? Thanks in advance, Eric Merkley

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decommissioning SGI Irix platform
by Eric Pettersen 29 Aug '08

29 Aug '08

Hi all, We are decommissioning our SGI machines as of 9/15, which means that the 1.2540 release was the last production release for SGI Irix. Daily builds will continue to be made for SGI until 9/15, so some post-1.2450 fixes/features will be available that way. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Povray and semitransparent maps
by odonnell＠chem.fsu.edu 29 Aug '08

29 Aug '08

Hi. I'm seeking a tip or two on how to save an image of a semitransparent map with PovRay. Povray works fine, but the image of the semitransparent map it generates is much darker that it appears on the screen. Any advice would be much appreciated. -Jason ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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ESP surface, DelphiController
by Elaine Meng 28 Aug '08

28 Aug '08

Hi James, Just because it has red, white and blue blotches does not mean it is showing ESP!! I don't think the different filenames in the DelPhi log are a problem - I believe temp files are generated from the ones you specify and used in the calculation for technical reasons. However, I do not know the reason for the error and not getting any output. You could try using Help... Report a Bug in the Chimera menu - give more details, such as all the error messages obtained and what it says at the end of the DelPhi log file. The main difficulty with DelPhi and any ESP calculation program is that atom names need to match those in the DelPhi charge parameter files. If you want to use all the hydrogens, you have to either edit all the names in the DelPhi charge parameter file or write out your PDB beforehand and edit all of its atom names to match those in the DelPhi charge parameter file. I have found this to be well nigh impossible. In general many hydrogen names not match and your molecule gets a very large net negative charge. Chimera tries to name hydrogens according to current PDB standards, but these old DelPhi parameter files use a different set of names. Instead, I would just used the DelPhi parameter files "default.crg" and "default.siz" which ignore hydrogens and just plop positives on nonhydrogen atoms in Lys, Arg (maybe His and N-term, I forget) and negatives on nonhydrogen atoms in Asp, Glu (maybe C-term). It is impossible to tell what "half all red" and "half all blue" means. It depends on what levels you have specified to be displayed as red and blue. Maybe the APBS map is fine - try changing the values set to red and blue to larger magnitudes. If APBS writes some sort of log file I would look at that, see if there is a reasonable net charge. Again most of the trickiness is in getting the right charges assigned to the atoms. You could use the PDB2PQR server to get an input file for APBS (if you didn't try that already). <http://nbcr.sdsc.edu/pdb2pqr/> Another possibility is to use the webPIPSA server as mentioned in previous messages, e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/003006.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 27, 2008, at 7:58 PM, James Fethiere wrote: > Hi Elaine, > > Nice that you found what I did 6kkm away!!! thanks. However, I must > say that it does look artificial. I'm just desperate to get the > electrostatic look as nice as possible (just like the pictures in http://www.cgl.ucsf.edu/chimera/tutorials/maps08/exercises.html#esp) > and found that was the closest I could get. One example I'm trying > is on 1DH3 > > On this note, I did try the delphicontroller to get the true > potentials but cannot get it to work. I have installed delphi on > windows-XP and called it from within chimera with tool/ > surfaceanalysis/delphicontroller. I entered the path for the > executable and charge and radii files. When I run delphi, I get an > error with no output file generated and some strange parameters in > the log file: > > in(pdb, file="tmph4vkzc") This does not correspond to the chimera > model I have chosen > in(siz, file="tmplk_go0") same here; not the file specified > in(crg, file="tmpbg7nlz") same thing > AC = true > CS = true > PF = 60 > SC = 1.2 > PR = 1.4 > FC = true > LG = false > LP = false > PX = false > PY = false > PZ = false > BC = 4 > ID = 2 > ED = 80 > GC = 0.0 > IS = 0.0 > IR = 0.0 > NI = 0 > > P.S. I did addH before starting Delphi! Any idea of what is going > wrong? > > I also tried to run APBS and got a potential file. But when I read > it in chimera, I get strange looking surfaces with half all red and > half all blue!!! here again I could use some guidance. > > Thanks for your help. > > James > -- > James Fethiere, Ph.D. > Institut de Recherche en Immunologie et Cancerologie > Pavillon Marcelle Coutu, University de Montreal > 2900 edouard-montpetit > Montreal, Qc H3t 1J4 > Tel: 514-343-6111 ext. 0918/0919 > Fax: 514-343-5839 > james.fethiere(a)umontreal.ca

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unattended installation on Windows
by Nelson, Lisa 27 Aug '08

27 Aug '08

Hello, I am not a chimera user; I'm an IT person. I have been asked to provide this application for next semester on our walk-up Windows computers for students. I have downloaded the necessary Windows installation materials, but I cannot find any documentation about command line parameters for the installation process itself, and the installation executable does not appear to be one of the usual suspects that I'm familiar with. Specifically, I'm looking for a way to do unattended, silent installation from a batch file. Attended installation is not an option as there are thousands of computers involved. Thanks for any help anybody can provide. I am not on the chimera mailing list, so please send replies privately. (The "contact us" webpage appears to give me the option of e-mailing to this list even though I'm not a member, so since I have only this one question and no particular need to subscribe, I've done it this way.) Thanks, Lisa.

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selection
by James Fethiere 26 Aug '08

26 Aug '08

Hi, I'm trying to create a category for separate surfacing of chains in a session that has multiple models. The following command: _surfcat sh3 #7:.a, surf sh3_ returns mangled atoms specifier. This may looks trivial but I can't find the right syntax to specify both the chain and residues in the same command. Any idea? Thanks James

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mrc opaque faces
by Benoit Zuber 26 Aug '08

26 Aug '08

Hello, I have problem looking at maps in mrc format calculated with IMOD. In mesh or surface style, when I move "level" towards lower value, the outer faces of the volume gradually become opaque. When I set the level to the minimum I see a smooth rectangular parallelepiped. I can then zoom in and have the camera inside the parallelepiped. With these settings, no density is visible inside the parallelepiped, only its faces are visible. In 3dmod I checked the edges of the map: they have a variable density, and they are not all black, or all white. Has anybody got a clue of what's going wrong? Thanks Ben -- Benoit Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK

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Faster volume plane display
by Thomas Goddard 25 Aug '08

25 Aug '08

Optimization for tomogram display. I optimized volume plane display making flipping through size 2048^2 data planes run at 17 frames per second instead of the 1.2 frames per second in the last Chimera production release 1.2540. This is with solid style rendering (gray-scale) and with mid-range graphics cards (tested on Radeon X1600 and Radeon 9800 Pro). The improved performance will be available in tonights Chimera daily builds. http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom

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Re: [Chimera-users] density maps in chimera- question
by Tom Goddard 22 Aug '08

22 Aug '08

Hi Sarah, Chimera does not show sigma values for a crystal map in the volume dialog. It shows whatever values are actually in the map file. Here is a description of how to convert to sigma values: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html Chimera map display was primarily intended for electron microscopy, hence the deficiencies with crystal maps you are encountering. Allowing direct display of sigma values is item 153 on our requested features list: http://www.cgl.ucsf.edu/chimera/plans.html Tom Sarah Boyce wrote: > Thanks Tom. I also was wondering about the display options for the > density. How does the histogram display level correlate to the sigma > level of the map? > > Sarah

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electrostatic surface coloring
by James Fethiere 22 Aug '08

22 Aug '08

Hi, 1. is there a way to use the electrostatic surface coloring from the tools/surface menu, in a command file? It seems that it is only available through the menu? 2. I have a pqr electrostatic potential file calculated from the PCE server http://bioserv.rpbs.jussieu.fr/Help/PCE.html using MEAD. How do I get it into chimera? Thanks

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Dr. Simon Sauve is out of the office.
by Simon Sauve 21 Aug '08

21 Aug '08

I will be out of the office starting 2008-08-21 and will not return until 2008-09-03. You can reach me at simsauve(a)yahoo.ca during the ICMRBS conference. In case of an emergency, please contact Dr. Yves Aubin by e-mail or @ 613-941-6155

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