September 2013 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

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Chimera commands to record MD movies
by psu4＠uic.edu 11 Oct '13

11 Oct '13

Dear Chimera, Since we run a lot of Amber MD simulation in remote clusters, we wonder if there is any Chimera command that can record the Amber MD trajectories remotely and save them as avi (or any other movie file formats)? If this is feasible, then we don't have to download all the trajectories to local and make the trajectory movies manually. We have searched the Chimera user manual but didn't see any command. If there are related commands which we didn't see, please forgive us : ) Thanks. * There is a way to activate X11 forwarding and use remote Chimera GUI to do this, but it's extremely slow and prone to freeze the computer. Cheers, Henry

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font size in pull-down menus
by Boaz Shaanan 09 Oct '13

09 Oct '13

Hi, Is there a way to change the font size of the pull-down menus? For some reason on the Windows (XP) v.1.5.1 they seem smaller to me. Nothing in terms of graphics (or my eyesight) has changed since I upgraded to 1.5.1 recently. Thanks, Boaz 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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Re: [Chimera-users] Question about multi align viewer
by Elaine Meng 03 Oct '13

03 Oct '13

On Sep 20, 2013, at 9:33 AM, Sean Connell wrote: > Hello I was wondering if it is possible to calculate conservation statistics using only subsets of the aligned sequence. The reason I ask is that in my alignment I have differently families of proteins that have slightly different functions and I would like to highlight residues that are conserved in one subset but not in the other? > Hi Sean, Not directly. I believe you would have to create alignments of just those subsets. You could do that with some other program (including text-editor) before opening the alignment in Chimera, or you could do it in Chimera. Of course, keep the original file with the full alignment too! To edit in Chimera, open the full alignment and then from the sequence window menu choose "Edit... Delete Sequences/Gaps" and in the resulting dialog, choose which sequences to delete. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> You can then continue working with the subset alignment in Chimera, including saving it to a new file (sequence window menu "File... Save As"). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. your original message was in an attachment, which was kind of weird, but I could view it by just clicking the attachment

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how to write script that can run chemera command
by 张海平 30 Sep '13

30 Sep '13

Dear professor: I find a command "delete ligand" can delete ligand from a protein. Then I have thousands of protein contain ligands, how can I write a script to do this command automotically, Thanks for your kindly help. Best regard Haiping Zhang

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Editing Question
by Kirk Moldoff 30 Sep '13

30 Sep '13

Hi, I'm working with a pdb model 3ALQ. It is a Tumor Necrosis Factor and its TNFR receptor. I'd like to be able to turn off the bound TNF. Or select it for deletion. Can't figure how to do this. Any suggestions? Ultimately I'd like to be able to save just the TNFR as a .pdb file. Thanks, Kirk -------- Kirk Moldoff www.galeriekirk.com 609-252-9479

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Generating a PDB file
by Nathalia Varejão 27 Sep '13

27 Sep '13

To whom it may concern, I'm using the chimera to visualize a protein ligand docking, but I want to save the best model as a PDB file that I can use anywhere to perform other analysis, is it possible? For example, the pdb that I saved by the chimera do not open in PyMol viewer... Can you help me? Nathalia

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STL file questions
by David Gene Morgan 26 Sep '13

26 Sep '13

Hi, I have a couple of questions about the chimera STL files. I tried to open one using chimera to determine whether they contain any color information, but I wasn't able to open the file I just wrote. I don't care about that, but I would like to know if they contain color information. Is there any way to control the degree of tesselation when writing an STL file? In other words, some STL files are huge because they contain huge numbers of triangles (and some 3d printers can't handle overly large files). I am wondering whether it is possible to control the size of the output files, which is effectively asking if it is possible to control the number of triangles in the file, how finely sampled the model is, etc. (however one wants to describe that property). Finally, as I understand STL files, they are usually "unscaled" (i.e., the co-ordinate system describing the vertices of the triangles doesn't have fixed length units). Is that true for the STL files chimera creates? If I wanted to create two models with an accurate reflection of their relative atomic sizes, are there tricks I will need to employ? -- David Gene Morgan Electron Microscopy Center 320C Simon Hall IU Bloomington 812 856 1457 (office) 812 856 3221 (3200) http://bio.indiana.edu/~cryo

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Calculating SAS areas for selected residues for a whole trajectory of structures
by Harald Lanig 24 Sep '13

24 Sep '13

Dear Chimera users, I am currently using chimera to calculate the solvent accessible surface for several selected residues of a single structure (I am using the Attribute calculator with the formula sum(atom.areaSAS) to do this). Is there a way to apply this to a set of structures coming from a molecular dynamics trajectory? I am interested in how the solvent accessible surface of a set of residues changes during the simulation. Any hint is highly appreciated! Best wishes, -Harald -- ------------------------------------------------------------------------ PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 harald DOT lanig AT fau.de Fax +49(0)9131-85 26565 http://www.chemie.uni-erlangen.de/lanig ------------------------------------------------------------------------

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