- Chimera-users - RBVI Mailing Lists

Contour maps or step-gradient of volume map?
by Bullitt Esther 13 May '13

13 May '13

Hi, Is it possible to choose n levels of gray for a volume map? I'd like to make a known-thickness slice using clip, and then see that slice as a defined number of colors. I can kluge it by displaying the map 4 times at 4 contour levels, but is there a better way? thanks, Esther --- Esther Bullitt, Ph.D. Dept. of Physiology & Biophysics Boston University School of Medicine 700 Albany Street, Room W302 Boston, MA 02118-2526 Email: bullitt(a)bu.edu Telephone: 617-638-5037 Facsimile: 617-638-4041 http://www.bumc.bu.edu/phys-biophys/faculty/bullitt

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mask using volume contour surface
by gongpu zhao 13 May '13

13 May '13

Hi All, I have a question about volume contour surface in chimera. I have a density volume of a shell shape. I plan to use the outer contour surface of the volume to mask out all density encased by the outer surface in a tomogram. But instead, I could only mask out the density within the shell. I am wondering if I can make a surface model only using the outer surface. Thanks a lot. Gongpu

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About Morph Conformations
by 吕柯 13 May '13

13 May '13

Dear Sir./Madam, I am a graduate student in Chinese Academy of Sciences. I have two PDB files: one for virus(4 chains, PDB:3VBS), the other for empty particle(3 chains, PDB:3VBU). I would like to use Morph Conformations to make movie for that. However, it turns out "Can not interpolate models: models have different number of chains". Could you please show me what should I do next? Thanks a lot. Yours, Lyu Ke -- Lyu Ke, Ph.D. student Structural Virology Unit Institut Pasteur of Shanghai Chinese Academy of Sciences No.411 Hefei Road Shanghai, 200025, P.R. China Tel: +86-21-54920652

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Re: [Chimera-users] saving sessions
by Tom Goddard 08 May '13

08 May '13

Hi Thomas, There is no session saving option that copies density map files to the same directory as the session file. All other Chimera models including PDB files are included (not linkied) in the session file. The reason maps are not put into the session file is because they are sometimes very large, Gbytes in size. Some day I intend to add an option to include the maps in the session file so you can have a self-contained session if you want. Copying the files could be another approach but it has problems. What if there is already a map with the same file name in the current directory? Could modify the copied file name I guess. Maybe better put all the map files in a new subdirectory. But are you really going to make copies of all the map files on every session save? If you only do it sometimes it doesn't solve the problem of moving data to a new computer. It will be slow to copy the files and it makes many redundant copies which then can become confusing as to whether two files with the same name really are identical. Hard links could be used to avoid copying the file, but that won't work when a session is on one file system and data on another. I think the way to handle moving data files to a new computer is to keep all your data including sessions under one directory tree so the whole thing can be easily copied. If instead the goal is to occassionally make a self-contained session then copying the map files and session file to a new directory would be a nice option similar to embedding all files in the session. I've noted this in the feature request for embedding the map files. http://plato.cgl.ucsf.edu/trac/chimera/ticket/9763 The sphere/axes display idea is one way to see the axes of a displayed model. The transparent sphere would cause problems in Chimera some of the time because Chimera can only correctly display one transparent model at a time. The current default is to show a single transparent layer, so any transparent model inside the sphere would disappear. This is a longstanding and hard problem to fix. But a mesh could work. Another idea is simply to depict the x,y,z axes. I've made a feature request for this. http://plato.cgl.ucsf.edu/trac/chimera/ticket/12062 Tom On May 8, 2013, at 12:25 AM, "Marlovits,Thomas" wrote: > Hi Tom, > > I do have a question related to saving sessions, which is a great option btw. > Is there a way that one can save the session - let's say in a new folder but then have all models also saved in there. For now, as I understand, it will only save the path/filename of those models. So, whenever we switch computers, hard-drives etc … this can turn out to be a lengthy process to find those models (we often have many models open at the same time). > Ideally, also fetched files from the pdb would be great to be saved locally in this new folder. > > The second question I have is related to turning molecules around specific x/y/z angles. > I'd love to have an option to display a big sphere that encapsulated the other models displayed. Ideally, this sphere would look like a globe with cordinates in there … if this is displayed at semi-transparency, one can easily go to a specific position but get more of an idea to easier naviagte through the 3D space. Sometimes I only would like to get a rough estimate about the angles to turn molecules. Alternatively a mesh-like grid could do the same job (and if one could display the numbers of the lattidude/longitude or so that would be great too). > > Many tx, > -T. > > > ------------------------------------------------------------------------------- > > Thomas C. Marlovits, PhD, M.A.S. > The MarlovitsLab @ IMP/IMBA > http://thomas.marlovits.myresearchlab.org > > Contact/Address/Directions: > http://thomas.marlovits.myresearchlab.org/lab/Contact.html >

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Define centroid issue
by Francesco Pietra 08 May '13

08 May '13

Hello: I was unable to put to work define centroid radius 0.5 color red :ligand_residue_name or define centroid radius 0.5 color red #0&@serialNumber=1972 with a homodimeric protein (I am at CHARMM NAMD/XPLOR, so that the two subunits are only distinguished by either the atom sequential number or the segment name, the latter not being understood by chimera, as far as I know). In the first case, running the movie after the appropriate further steps, the centroid sequence obtained was for the centroid between the two protein ligands, as it was expected. In the second case (as I wanted to refer to the ligand in subunit A only), the command raised the error: AttributeError: 'NoneType' object has no attribute 'openState' File "/opt/UCSF/Chimera64-1.7/share/StructMeasure/Geometry.py", line 293, in _getRefInfo invXForm = lowest.openState.xform Please notice that the line command #0&@serialNumber=1972 correctly selects the ligand on subunit A (a diatomic ligand, where "1972" is the sequential number of one of the two atoms of the ligand. Here "#0" may be redundant, as it deals of a single model. However, using "@serialNumber=1972" raised the same error. I fear I am missing some obvious facet of define centroid, so that I thank you for your patience. francesco pietra

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Question about measuring volume in chimera
by Varun Kumar 07 May '13

07 May '13

Hi, Can we outline a particular area and measure volume in chimera? I wish to measure specifically the purine binding site in the ATP binding pocket of Protein kinase C. Best regards -- Varun Kumar International Graduate Student School of Biomedical Sciences Department of Biological Sciences Kent State University, Kent, Ohio, U.S

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RMSD
by George Tzotzos 04 May '13

04 May '13

Hi everybody, I am trying to measure the RMSD between a docked ligand and the corresponding ligand in an X-ray structure. I've been looking to find a way of doing this in Chimera to no avail. I'd be grateful for any suggestions on how to do this. Best regards George

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save map with the adjusted threshold
by Moumita Dutta 01 May '13

01 May '13

Hello, I'm not sure if I can do this in chimera. Once I open a density map and adjust the threshold and removed dust how can I save the map in this setting so that next time when I open it I don't have to adjust again. Thanks

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Chimera shutsdown when opening sideview
by vamsee 29 Apr '13

29 Apr '13

Hi Elaine, I have recently moved to Linuxmint 14 from Windows 7. I can open virus capsids very easily (much more easier than in Windows 7, which is pretty sweet). But, every time I try to open the Side View option from the menu, Chimera shuts down. I have tried version 1.7 and 1.8rc. Both exhibit the same behavior. The interesting thing is, I can open all the other tabs (Effects, Lighting etc.) on that window from the menu. But when I click on Side View, Chimera crashes immediately with no bug report (Its almost like the process never existed). So, I tried starting chimera from the command line with the Side View option enabled (sudo chimera --start "Side View"). That started the Side View window and that stayed even after I opened my models. I then closed the Side View and re-opened it from the menu bar this time in the same chimera session. That worked again. So, I am kind of at a loss though I seem to have a work around for now. I have used the same features on Windows 7 (I still do using a virtual machine inside Linux) and they work fine. Any reason why this would happen? My computer specifications Processor : Intel® Core™ i7-2630QM CPU @ 2.00GHz × 8 Memory : 8Gb Onboard Video : Intel® Sandybridge Mobile OS : LinuxMint 14 Thank you Vamsee

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morph conformation
by Moumita Dutta 27 Apr '13

27 Apr '13

Hello chimera-users, I'm trying to use the option morph conformations from the command line and cannot specify more than one molecule with the command morph start. How to use the morph start command for more than two molecules ? Thanks for any help. Moumita

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