- Chimera-users - RBVI Mailing Lists

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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