June 2010 - Chimera-users - RBVI Mailing Lists

Lost hydrogens when saving mol2 file
by Varela, Lawrence Rocco 23 Jun '10

23 Jun '10

I'm encountering a problem where I'm loosing hydrogens from my small molecules after saving them in Chimera. Here is the situation: the original mol2 file I open has a number of small molecules listed under separate MOLECULE tag identifiers. Using the GUI menu I select "save Mol2", select all the models to save, and select the Save multiple models in "a single file [combined @MOLECULE section] option. When I open the newly saved Mol2 file with the combined MOLECULE section it's obvious that the hydrogens have been removed. How do a save multiple models in a combined MOLECULE section without loosing any hydrogen atoms? Thanks :-) Rocco

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PDB
by Dougherty, Matthew T 23 Jun '10

23 Jun '10

Hi, When PDF files are read by Chimera and the session is written, the PDB data becomes part and parcel with the session files. That is, Chimera does not go back to the PDB files when it reloads the session, it uses the PDB data within the session file instead; as contrasted to density volume files, which are referenced by the session file, and the density volume files reloaded when the session file is read by Chimera. Is there a way to force the session file not to save the PDB internally to the session file, and instead reference and interact with it similar to the way volume files are managed? Matthew

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Grouping Molecules
by Varela, Lawrence Rocco 23 Jun '10

23 Jun '10

Is there a way of grouping molecules in Chimera? Here is my situation. I have 4 molecules A, B, C, and D and I want to group A with B and C with D so that A and B has one center of rotation and C and D has another center of rotation. Rocco

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Fwd: Chimera 3-D viewing
by Eric Pettersen 21 Jun '10

21 Jun '10

Forwarding Ed Pate's question (below) to this list, in the hope that someone who actually knows the answer can chime in! --Eric Begin forwarded message: > From: Edward Pate <edpate(a)hotmail.com> > Date: June 19, 2010 2:39:09 PM PDT > To: <pett(a)cgl.ucsf.edu> > Subject: Chimera 3-D viewing > > Hi Eric: > > I am looking into getting a new workstation for Chimera. In the > past, we have gotten CRT displays in order to do 3-D visualization. > Could you recommend other display options that are available now and > that users have been happy with? Is a CRT still the best option? > > Thanks for the help. > > Ed

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vop binning
by Katrina Lexa 21 Jun '10

21 Jun '10

Hello - Is the volume data (vop) code available somewhere? Particulary the code for binning electron densities? I'm interested in looking at how chimera handles xplor files since I want to find the density of solvent at the edges of my grid. I would love to try to play with the volume code in order see if it can be done through chimera. Thank you, Katrina

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Re: [Chimera-users] Chimera -RMSD
by Eric Pettersen 21 Jun '10

21 Jun '10

On Jun 21, 2010, at 6:25 AM, S. Shunmugasundararaj wrote: > Dear Eric, > > I am using Chimera v1.4. When aligning 2 or more structures, it > gives the > RMSD as a bar graph. Is it possible to get the RMSD value for each > residue? > > Thanks > Raj Hi Raj, I'm guessing the "RMSD as a bar graph" is the RMSD header at the top of the Multalign Viewer tool. You can save the header values to a file with the "Headers->Save..." menu entry at the top of the tool. This will save the RMSD value for each alignment position to a file. This may or may not be useful for you since the residues associated with each alignment position aren't indicated in the file. Alternatively, each residue involved in the Multalign Viewer RMSD header calculation gets a "mavRMSD" attribute assigned to it. You can save these attributes to a file by using the "File->Save Attributes..." menu of the Render By Attribute tool (available in the Depiction and Structure Analysis tools menus). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Error running chimera
by Christian Hesketh 21 Jun '10

21 Jun '10

Hi there, I have been able to use Chimera many times in the past, but now when I try to run it, a dialog box pops up and I get get any further. In fact, it seems to be spawned infinitely and I cannot close it. Here is the message: "Class DBPuppet.AC_KEY_ERROR'> Can't open web info file for reading". I don't know what has changed on my system to cause this, it was working fine a week ago. Does anyone have any ideas? I am using the most stable production version right now. My operating system is Windows Vista. Thanks in advance, Christian

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total sum of a map
by Mario Dejung 21 Jun '10

21 Jun '10

Hi all, I try to multiply two maps in chimera. At the moment my workflow is the following: *open my two maps in chimera and try to fit map into map... *then I use "vop resample #1 inGrid #2" to set the same orientation *after this step, I convert the mrc files to Imagic and do a total-sum *what I get is one volume. Isn't there a way to do this in chimera? Thanks to all for any suggestions. Kind regards Mario

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Rendering solid objects and POVRAY
by Mario J. Borgnia 16 Jun '10

16 Jun '10

Hi, I am trying to render an image that includes a difference map density displayed as a solid object. When I try to get the image directly from the screen it shows patterns of pixelation. I then tried POVRAY and the solid object data does not show up. Is there anything that I am missing? Thanks -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia(a)nih.gov | +---------------------------------+

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Open dialog box
by Rocco Varela 15 Jun '10

15 Jun '10

Is there a way to change the look-and-feel of the GUI open dialog box? Every time I try to open a file using the File>Open option in the GUI menu I'm faced with the problem of not being able to see the entire file names in the file navigator window. Enlarging the size of the open dialog box doesn't seem to resolve the issue. -Rocco

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Chimera-users June 2010