- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [chimera-dev] Hydrophobicity
by Elaine Meng 18 Sep '08

18 Sep '08

On Sep 17, 2008, at 10:14 PM, Leo O'Young wrote: > > I am new to the list, I am wondering if it is possible to increase > the geometry > of the Hydrophobicity-Surface models. > > Thanks, > Leo Hi Leo, Welcome! The "hydrophobicity" in the preset is just a coloring scheme, so I will set that aside and discuss molecular surfaces. I am not sure what you mean by "increase the geometry." There are several ways you can adjust molecular surfaces in Chimera: change vertex density, probe radius, and also the radii of the underlying atoms. It is a molecular surface by the Richards definition, also known as the solvent-excluded surface, made of probe contact and re- entrant patches; it shows the VDW surface of the structure except with crevices smoothed. Currently Chimera does not show the solvent- accessible surface, which is where the probe center goes. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces > If you mean you want to make the surface "bigger" to enclose a greater volume, that can be done by increasing the VDW radii of the atoms, and to a lesser extent, increasing the probe radius, which will smooth the crevices more. One way to increase VDW radii is with a command; this would increase all radii by 0.7 A, for example: vdwdefine +0.7 (the command ~vdwdefine changes the radii back to defaults). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html#changing > To change probe radius or other parameters of an existing molecular surface: - Ctrl-click the surface to select it - open the Selection Inspector (click the greenish button on the lower right corner of the Chimera window or choose Actions... Inspect from the menu) - in that dialog, Inspect "MSMS surface", and then edit the various parameters as desired <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html#msmsprop > You can also set preferences to use different parameters for surfaces created in the future, so you don't have to change each one after you create it. To do that, choose Favorites... Preferences, go to the New Surfaces category, change parameters as desired and click Save. That only pertains to surface parameters, not VDW radii of atoms, however. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surf… > 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 _______________________________________________ Chimera-dev mailing list Chimera-dev(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Protonating ASP and GLU
by Francesco Pietra 18 Sep '08

18 Sep '08

Is there any special reason why, in the AddH option, side chains are only considered for HIS (with full options)? Why similar options are not given to protonate GLU and/or ASP at the carboxylate? The general option to consider H-bonding does not work in my case for such residues close to one another in space with Chimera (the two O atoms of two ASP residues are at 2.56A from one another). Even Reduce, supposed to protonate close lying carboxylates, failed in my case. This is why I would consider to add that option in future versions of Chimera. Thanks francesco pietra

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heavy black awful nuisance grid
by Barry Lever 16 Sep '08

16 Sep '08

AS a new user of Chimera, I apologize for asking what , for many of you, is probably a trivial question.... initially when using Chimera ,creating an image (using pseudobond Reader) and then saving an image file, (save image) all worked well, but in the last couple of days, every time I save an image file in whatever mode (png, tif, jpg etc), I get my image with a heavy black grid across it.(and on two different computers). I am using Chimera 1.254. Is there a simple fix- it feels like a conflict. I attach one of the images Thanks for your help (Windows XP, SP3) Barry -- A. B. P. Lever Distinguished Research Professor Emeritus Chemistry, CB124, York University 4700 Keele St., Toronto, Ont., Canada M3J 1P3 Tel:416-736-2100 x22309 Fax: 416-736-5936 http://www.chem.yorku.ca/profs/lever

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solaris version
by o.h.weiergraeber＠fz-juelich.de 16 Sep '08

16 Sep '08

A question to the chimera developers: Having used chimera for several years on IRIX and Linux machines, we can say it is maybe the most useful tool available for molecular visualization and related purposes. However, most important (freeware) packages in the field of x-ray crystallography have also become available as Solaris(x86) versions over the past few years. In my opinion it is quite an attractive platform mainly because it avoids all the confusions and incompatibilities arising from the multitude of distributions in the Linux world. Thanks to the overall conceptual similarity to Linux compilation should (in principle) not run into tremendous problems. I would try myself, but the source code available is not complete afaik :( So, are there plans for a Solaris version of chimera in the near future? In previous discussions on this mailing list I found there are even some Solaris-related comments in the source code ;) Greetings Oliver ------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 ------------------------------- ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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Pyrazine problem
by Francesco Pietra 15 Sep '08

15 Sep '08

Hi: I am dealing with pyrazine compunds in view of docking with DOCK6. The two nitrogens proved problematic for Chimera so that, to simplify, I tried with pyrazine itself, getting the same problems. I used for getting the pdb the MM package I am familiar with: 1. draw benzene, 2. replace two para carbons with N, 3. replace the H on N with a lone pair. The two nitrogens are now indicated of MM3 (or MMX) type 37 (-N=C-/PYR (DELOCALIZED). The charge on the nitrogens is 0.15, on the lone pairs -0.21, on carbon 0.14, on H 0.04. Save as pdb, load to Chimera, then Tools, Structure editing .. Add charge, it results total charge -2. In fact, commanding addH adds a hydrogen to each nitrogen and the resulting molecule is neutral, while it should be +2. If in Chimera I save the loaded pdb as mol2, the two nitrogens result of Tripos type N.pl3, i.e., trigonal planar nitrogen, which is the wrong type. Naively, I replaced N.pl3 with N.ar (aromatic nitrogen) in the mol2.file, getting the same results on reloading the mol2. So the two packages, MM and Chimera are internally consistent but (for the first time in my experience with both packages) they are not mutually consistent. I tried to build pyrazine atom-by-atom, getting the same results. Attached is the pdb and the mol2. When opening the pdb, Chimera says: "Ignored bad pdb record found on line 26"; actually there are fewer than 26 lines. Thanks for help francesco pietra

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Re: [Chimera-users] rotational/translational shift from reference structure
by Elaine Meng 15 Sep '08

15 Sep '08

On Sep 15, 2008, at 3:13 AM, julien(GWDG) wrote: > > I wanted to know if there is a way in chimera to get the same > information as the shortcut ai but for small molecule. > When I use "ai" with small molecule I get the message : "not enough > back bone atoms", which is normal because there is no back bone atom > and because the molecule is small. > But I have a rigid docking of one ligand and I would like to see > what is the rotation components (rotation matrix) between the > different pose. Of course one could just do it by a small C++ script > but if chimera has it already implemented it would be easier for us. > > Thank you for your support and your nice soft. > > many greetings > > Julien > Hi Julien, Thanks for the compliments! There are commands to do a similar thing, although not in one step. The "match" command will fit the specified atoms and give an RMSD. Unlike the ai shortcut, it moves one structure onto the other. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> Then you can use the "matrixget" command to report the transformations of the structures. However, note this reports the total transformation: all movements that have been applied, not just what happened in the fitting step. To get only the fitting transformation, you would first need to "reset" the reference structure so it is untransformed, then "match" the other structure onto it, then use "matrixget." <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html> For example, using two different structures with FAD: open 1f3p open 2npx focus preset apply int 1 reset match #1:fad #0:fad matrixget - Don't move anything around by hand between "reset" and "matrixget"! The last command sends the matrix info to the Reply Log. In this case the atoms in FAD are ordered and named consistently, so I could simply use the residue name in the match command. If you only wanted to use certain atoms, or if the atoms were not ordered and named consistently, you would have to give the atom names in the match command. 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] trouble installing linux i386 executable
by Eric Pettersen 15 Sep '08

15 Sep '08

Hi Blake, I've certainly had problems that "solved themselves" like that. :-) I hope further use of Chimera is less mysterious! --Eric On Sep 15, 2008, at 12:55 PM, Blake Mertz wrote: > Eric, > > Thanks much for looking into that for me -- actually, I came back to > my machine the next morning, ran the install command exactly as > specified on the website, and it ran this time. I swear I wasn't > hallucinating when I sent that message, so thanks again for taking > the time. I'm definitely looking forward to using Chimera, as a > former student in our research group had nothing but good things to > say about it. Talk to you soon. > > Blake > > On Mon, Sep 15, 2008 at 11:46 AM, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: > Hi Blake, > _Seems_ like it should work. Running from the directory with the > Chimera installer, what is the output of the following commands: > > df . > sudo pwd > sudo ls -l > sudo ls -ld . > sudo ls -ld .. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Sep 10, 2008, at 2:33 PM, Blake Mertz wrote: > >> Hi, >> >> My name is Blake, and I'm a postdoc at the U. of Arizona. I'm >> starting >> to use Chimera after using Pymol for a long time, but have had >> trouble >> getting it installed. After downloading the .exe file and changing it >> to an executable, here is the error message I get: >> >> blake@omega:~/Desktop$ ls -l chimera-1.2540-linux.exe >> -rwxr-xr-x 1 blake blake 97898302 2008-09-10 14:12 chimera-1.2540- >> linux.exe >> blake@omega:~/Desktop$ sudo ./chimera-1.2540-linux.exe >> [sudo] password for blake: >> sudo: unable to execute ./chimera-1.2540-linux.exe: No such file or >> directory >> >> There has to be something obvious I'm missing here, correct? I'm >> running Ubuntu v. 8.04, if that helps. Thanks, and talk to you soon. >> >> Blake >> >> -- >> Research Assistant >> Department of Chemistry >> University of Arizona >> >> "Life is not easy for any of us. But what of that? We must have >> perseverance and above all confidence in ourselves. We must believe >> that we are gifted for something and that this thing must be >> attained." Marie Curie >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- > Research Assistant > Department of Chemistry > University of Arizona > > "Life is not easy for any of us. But what of that? We must have > perseverance and above all confidence in ourselves. We must believe > that we are gifted for something and that this thing must be > attained." Marie Curie

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trouble installing linux i386 executable
by Blake Mertz 15 Sep '08

15 Sep '08

Hi, My name is Blake, and I'm a postdoc at the U. of Arizona. I'm starting to use Chimera after using Pymol for a long time, but have had trouble getting it installed. After downloading the .exe file and changing it to an executable, here is the error message I get: blake@omega:~/Desktop$ ls -l chimera-1.2540-linux.exe -rwxr-xr-x 1 blake blake 97898302 2008-09-10 14:12 chimera-1.2540-linux.exe blake@omega:~/Desktop$ sudo ./chimera-1.2540-linux.exe [sudo] password for blake: sudo: unable to execute ./chimera-1.2540-linux.exe: No such file or directory There has to be something obvious I'm missing here, correct? I'm running Ubuntu v. 8.04, if that helps. Thanks, and talk to you soon. Blake -- Research Assistant Department of Chemistry University of Arizona "Life is not easy for any of us. But what of that? We must have perseverance and above all confidence in ourselves. We must believe that we are gifted for something and that this thing must be attained." Marie Curie

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(Thermal ellipsoids) anisotropic temperature factor ellipsoids
by David Chenoweth 15 Sep '08

15 Sep '08

Dear Chimera team, Does Chimera have the ability to display anisotropic temperature factor ellipsoids and if not can this feature be added? Thanks in advance, Dave Chenoweth ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen(a)caltech.edu **********************************************

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Crash with Intel graphics on Windows fixed
by Greg Couch 12 Sep '08

12 Sep '08

We have been seeing a large number of bug reports from Windows laptops with Intel graphics (both XP and Vista, as well as desktop systems) with the lastest chimera production release, 1.2540. The symptoms include, but are not limited to, jumbled surface triangles, incorrect lighting, "unable to share data" errors, wglMakeCurrent failures, "pure virtual function called", and the inability to exit chimera. The bug has been isolated to the Intel graphics driver and a workaround has been added to chimera. The fixed version of chimera is available today in the Daily Builds section on the chimera website, <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html>. Greg Couch UCSF Computer Graphics Lab

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grid across graphic
by Barry Lever 11 Sep '08

11 Sep '08

AS a new user of Chimera, I apologize for asking what , for many of you, is probably a trivial question.... initially when using Chimera ,creating an image (using pseudobond Reader) and then saving an image file, (save image) all worked well, but in the last couple of days, every time I save an image file in whatever mode (png, tif, jpg etc), I get my image with a heavy black grid across it.(and on two different computers). I am using Chimera 1.254. Is there a simple fix- it feels like a conflict. Thanks for your help (Windows XP, SP3) a low resolution example is appended Barry -- A B P Lever Distinguished Research Professor Emeritus York University, Chemistry CB124 4700 Keele St., Ontario, Canada, M3J 1P3 Tel: 416-736-2100 x22309 Fax: 416-736-5936 http://www.chem.yorku.ca/profs/lever

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rotational/translational shift from reference structure
by KATRYNA CISEK 11 Sep '08

11 Sep '08

Dear Chimera developer, I would like to analyze a set of dimer structures based on a reference dimer structure. Unfortunately a simple RMSD calculation does not capture the translational/rotational shift that occurs. Is it possible to extract a plane of rotation and degree of rotation between two structures in chimera? Thanks, Katryna

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rmsd in nogui mode
by Ryan 10 Sep '08

10 Sep '08

Hi again, I'd like to save the rmsd values calculated by chimera's 'rmsd' command when running in 'nogui' mode. What's the best way to go about this? Thanks! -ryan

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addh question
by P. Law 10 Sep '08

10 Sep '08

Hi, I am analyzing water-water and water-protein hydrogen bonds in a dataset of high resolution crystal structures. As part of this analysis, I will need to add hydrogens to water molecules and to the protein. I was wondering how well the "addh" tool can place hydrogens on water molecules in the first shell around the protein? If addh is not the right tool for this task, are you aware of any freely available programs that can add hydrogens to 1st shell water molecules in PDB files? Thanks for your help! Sincerely, Peter Law Graduate Student Biochemistry Department University of Washington

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importing general 3D models into Chimera
by Jeff Triffo 09 Sep '08

09 Sep '08

hi users, I figure someone on this list has run across this before. I have been using a modeling/CAM tool - Rhino - to generate a 3D model that I would like to import into Chimera, if possible. Does anyone have a "best way" to go about doing this? Rhino is a NURBS modeler that will export as .dxf or .dwg (AutoCAD), .ai (Adobe Illustrator), .fbx (MotionBuilder), .obj (Wavefront), .igs/.iges (IGES), .sat (ACIS), and .stl (Stereolithography). It also saves in its native format - .3dm - but that is a NURBS (openNURBS) format and I realize that Chimera does not render NURBS. Of the export options above, having limited familiarity with Illustrator, I am unsure what the nature of "3D" is in that format. thanks for any suggestions, -Jeff

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surface capping command
by Gabriel Lander 09 Sep '08

09 Sep '08

Is there a way to turn on surface capping from the Chimera command line?

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saving images -- wire representation at higher dpi
by Ryan 09 Sep '08

09 Sep '08

Hi, I am trying to save higher resolution images that contain some residues with a wire width of 2. I have noticed that when i increase the dpi of the images, the saved images look different than what is displayed in the viewer -- nodes appear at each atom of the residues that are displayed as wires. As i increase the dpi of the saved images, the nodes become increasingly exaggerated (of a thicker radius than the wire bonds). Is this what should be happening? If so, is there a way to have both the atoms and bonds save with the same radius? Thanks a lot, ryan

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Models or chain
by hsosa＠aecom.yu.edu 09 Sep '08

09 Sep '08

I have created a model from several PDB files and saved it using the save PDB utility in chimera. The resulting PDB file had the different molecules separated in the PDB file with the lines MODEL 1 . . . MODEL 2 . . . MODEL 3 . . . and so on. Is it possible instead to save the PDB file as one model but using different chain names for the different molecules ?. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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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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emulation of threee button mouse not working
by Geeta Narlikar 21 Aug '08

21 Aug '08

Hi, I'm having problems with the three button mouse emulation feature. My OS is Mac X Leopard and I turned on the "emulate three button" mouse feature in X11. But that does not seem to work. My version of Chimera is 1.2509. Is there any other setting I should change? Thanks for your help. Geeta Narlikar

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Re: [Chimera-users] density maps in chimera- question
by Thomas Goddard 21 Aug '08

21 Aug '08

Hi Sarah, You can use the keyboard shortcut "bv" to create a new map that covers your PDB model. To enable keyboard shortcuts use Tools / General Controls / Keyboard Shortcuts and turn on "Enable keyboard shortcuts" in the dialog. Select the atoms of your PDB model. If you have more than one map open make sure the highlighted one in the volume dialog is the crystal map for the selected atoms. Then type the "bv" shortcut to create a new map covering the select atoms. This assumes that the starting map is a full unit cell. If you don't want to go to the trouble of enabling keyboard shortcuts, you can use the command "ac bv" which runs the shortcut (accelerator) bv. You can save the covering map with volume dialog File / Save Map As.... Tom Sarah Boyce wrote: > Hi Tom- I was told you might be the person to ask about the density map > features in chimera. I'm trying to display crystallographic electron > density maps and I've run into a problem aligning some of the maps to > the protein model. When I load the map and model it looks as though the > map is of the symmetry related molecule, but when viewed using Coot it > automatically centers the map on the model. So far the only tool that > I've found to do this is by hand alignment, which doesn't work at all > for an atomic level model (or at least when I've tried it it is too much > of a pain). Is there an automated tool in chimera that will > automatically center the map on the model similar to the way Coot > handles it? > > > Thanks, Sarah

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(no subject)
by charles marchand 21 Aug '08

21 Aug '08

Greetings, I was wondering if someone could tell me how to select multiple sequences in the sequence viewer. I am trying to select different regions of RNA to visualize, but Chimera has not allowed me to pick to sequences that are separate. Is there a way to do it through the sequence viewer? Thank you, Charlie

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Re: [Chimera-users] CHARMM PBEQ calculations
by Tom Goddard 21 Aug '08

21 Aug '08

Hi Fabian, The OpenDX file you sent has a small but important error. It is missing the words "data follows" at the end of the header line that says "object 3 class array..." so Chimera never reads the data. The misleading error message comes about because the last line of the file is blank and Chimera still thinks it is reading the header. The header line object 3 class array type double rank 0 items 378885 has to be object 3 class array type double rank 0 items 378885 data follows Hopefully Sunhwan can update the phi2dx.py script to include the very important "data follows". The OpenDX format is described in Appendix B of the OpenDX User's Guide: http://opendx.npaci.edu/docs/pdf/userguide.pdf Tom Fabian Glaser wrote: > Dear Elaine, > > I am afraid it's still giving the same error when I try to open the dx > file, even when the first line is removed or # starts it. Here is the > message: > > Opening /media/data/WORKSPACE/PROJECTS/DanCassel/COP/step2_pbeq.dx > Error reading file step2_pbeq.dx, format apbs > Incorrect format: blank header line. Comments must begin with # > character. > > And the dx file is attached, probably I am doing something wrong.... > > THanks a lot, > > Fabian > > > Elaine Meng said the following on 19/08/08 19:19: >> Hi Fabian, >> Well, the error message says the format is wrong. Based on the >> message, you could try removing the blank line at the top of the file >> or adding # in front of it. >> >> If that still doesn't work you could send me the file to look at, but >> it is probably just a simple fix such as the above. >> 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 19, 2008, at 7:03 AM, Fabian Glaser wrote: >> >>> Dear Sunhwan >>> >>> Thanks a lot for your kind answer and for the script. The script run >>> fine, but when I try to upload it to chimera I get an error: >>> >>> Opening >>> /media/data/WORKSPACE/PROJECTS/HaimManor/EladEliahoo/MODELS/POMBE/CHARMM-PBEQ/charmm-gui/step2_pbeq.dx >>> >>> Error reading file step2_pbeq.dx, format apbs >>> Incorrect format: blank header line. Comments must begin with # >>> character. >>> Done opening >>> /media/data/WORKSPACE/PROJECTS/HaimManor/EladEliahoo/MODELS/POMBE/CHARMM-PBEQ/charmm-gui/step2_pbeq.dx >>> >>> >>> Which maybe perfectly chimera problem, so I am CCing this email also >>> to Elaine Meng from the CHIMERA team. >>> >>> Any help will be very appreciated, >>> >>> Thanks a lot, >>> >>> FAbian >>> >>> Sunhwan Jo said the following on 19/08/08 15:25: >>>> Dear Dr. Glaser, >>>> >>>> I'm afraid CHIMERA is not able to read CHARMM phi80 format. But simple >>>> search guided me that CHIMERA can to read dx format file, which I >>>> have a >>>> converting script. So, please find the script in the attached file. >>>> We've been >>>> using this script to read our potential data in Pymol, so I believe >>>> this should >>>> be working fine with CHIMERA as well. >>>> >>>> usage: >>>> python phi2dx.py step2_pbeq.phi80 > step2_pbeq.dx >>>> >>>> Please feel free to contact me, if you have a further problem. >>>> >>>> Thanks, >>>> Sunhwan >>>> >>>> >>>> On Tue, Aug 19, 2008 at 4:53 AM, Fabian Glaser >>>> <fglaser(a)technion.ac.il> wrote: >>>> >>>>> Dearl CHARMM team, >>>>> >>>>> have been trying to upload the electrostatic potential calculated >>>>> by CHARMM PBEQ routine to the CHIMERA viewer, since the java >>>>> viewer you use is very good but at least in my machine does not >>>>> work. But despite I have been trying to upload it to chimera there >>>>> seems to be some stubborn problem (or I am doing something wrong). >>>>> What I am trying to do is to color the pdb by the potential in >>>>> chimera so I can freely manipulate it and compare it with other >>>>> calculations. >>>>> >>>>> If you have any suggestion I'll be very grateful, >>>>> >>>>> Best regards, >>>>> >>>>> Fabian Glaser, PhD

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clipping planes question
by William Jeffrey Triffo 20 Aug '08

20 Aug '08

I know of the hinder and yon clipping planes, and also the per-model clipping plane that allows individual model clipping. I have a current imaging session where I have already used per-model clipping on several models, but would like to trim off some material from the side of the entire combined model - I don't suppose there is an arbitrary clipping plane that applies to the whole scene, like hinder-yon but from any user-defined direction? For now, I was just going to crop the resulting image. But this will result in an abrupt end to the background color (I can adjust the image border clone the background in photoshop/etc, but would be nice to be able to do that within Chimera) thanks, -Jeff

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saving nol2 files
by 吴超 20 Aug '08

20 Aug '08

Hi, dear folks, I have some doubt about how chimera determines the atom type when you save mol2 files from ligand pdb files. Because when I opened the saved mol2 files, I found there were some mistakes about atom type. Does Chimera use the same procedure that Sybyl uses to determine the atom type? -- Chao Wu

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MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ???
by Darrell Hurt 20 Aug '08

20 Aug '08

Hi there, I¹m trying to use the command MultiScale.color_surfaces_to_match_atoms(). I want to point out a mutation on the surface of a virus. I can color the atoms correctly, but I can¹t figure out how to apply that color to the MultiScale low-resolution surface. Any hints on how to use this command? Also, how can I increase the mesh resolution on MultiScale surfaces for input for 3D printing? Thanks! Darrell -- NIH Researchers: check out our new web site <http://inside.niaid.nih.gov/topic/IT/bioinformatics/Pages/default.aspx> Darrell Hurt, Ph.D. Section Head, Biocomputing Research Consulting Bioinformatics and Scientific IT Program (BSIP) NIAID Office of Technology Information Systems (OTIS) National Institutes of Health, DHHS Contractor, Lockheed Martin 4 Memorial Drive, Room 424 Bethesda, MD 20892-0485 Mobile: (301) 758-3559 Fax: (301) 402-0366 NIAID Intranet: http://bioinformatics.niaid.nih.gov <http://bioinformatics.niaid.nih.gov/> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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