December 2008 - 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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color scale bar
by Yao Cong 17 Jul '09

17 Jul '09

Hello Chimera developer, I am rendering a PDB file colored according to B-factor value by "render by attribute" tool. How can I generate a color scale bar besides the structure labeling the color scale used? Many thanks, Yao Cong

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sequence viewer
by Gatsogiannis, Christos 13 Jul '09

13 Jul '09

Hi all, i ve just installed the latest daily build version and i´ve noticed that the sequence viewer has a new "look". However, i have difficulties to get used to it... Some examples: -when i want to view the sequence of a pdb file containing seven chains, i get seven different pop-up windows (...) showing the sequences corresponding to the seven different chain ID´s.... -Moreover, it isn´t so "easy" anymore to select aminoacids directly in the sequence viewer (e.g. too many colors) and therefore now i´m selecting residues using only the command line.. My colleagues also prefer the older version.. is there a simple way to install the latest chimera version but keep the old version of the sequence viewer? Thanks! -Christos ------------------------------- Christos Gatsogiannis Insitute of Zoology, Dpt. II cryoEM Lab, AG Markl Joh. v. Müllerweg 6 Johannes Gutenberg University Mainz, Germany +49-6131-3923091 ------------------------------- ________________________________________ Von: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] im Auftrag von chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Gesendet: Mittwoch, 17. Dezember 2008 21:00 An: chimera-users(a)cgl.ucsf.edu Betreff: Chimera-users Digest, Vol 68, Issue 22 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: (Thermal ellipsoids) anisotropic temperature factor ellipsoids (Eric Pettersen) 2. Re: (Thermal ellipsoids) anisotropic temperature factor ellipsoids (Eric Pettersen) 3. possibilities to save parts of models (selection)? (Sebastian Kruggel) 4. Re: possibilities to save parts of models (selection)? (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 16 Dec 2008 14:59:34 -0800 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids To: Tom Goddard <goddard(a)cgl.ucsf.edu> Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> Message-ID: <9A34751B-6356-4AF4-A8C7-31757E5FFBF1(a)cgl.ucsf.edu> Content-Type: text/plain; charset="us-ascii" On Dec 12, 2008, at 10:40 AM, Tom Goddard wrote: > Hi David, > > Ok I see now, it's a matter of choosing the size of each ellipsoid to > have a 50% chance of finding the atom in that volume. This > shouldn't be > too hard but I'll let Eric tackle it if he has time. Hi David, This is one of those things that I'll endeavor to get into Chimera's production version of thermal ellipsoids, but that I can't spare the time for until then. My guess is that the eigenvectors/values of the U matrix are at the 50% probability level, but verifying that would require some research. If you do look into and find that that's not the case, just change the setting of the 'scale' variable of the start of the script to change the ellipsoid sizes to whatever size encloses 50%. --Eric

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delphi
by Darren Thompson 06 Jan '09

06 Jan '09

I installed the ibm compiler libraries on Mac OSX tiger, but delphi still does not see them Applications System Folder mach.sym Applications (Mac OS 9) TheVolumeSettingsFolder mach_kernel Desktop (Mac OS 9) Trash opt Desktop DB Users private Desktop DF Volumes sbin Desktop Folder automount sw Developer bin tmp Documents cores usr Library dev var Network etc System mach the opt folder (ibm) is there. I did a symbolic link to the Mac OSX executable in the /usr/local/ release1.1/exe directory to /usr/bin/delphi, downloaded the example files from delphi's website, [psb-232-45:release1.1/examples/example_1] darren% delphi param_1 dyld: Library not loaded: /opt/ibmcmp/lib/libxlf90.dylib Referenced from: /usr/bin/delphi Reason: image not found Trace/BPT trap when I try directly [psb-232-45:local/release1.1/exe] darren% ./delphiMacOSX dyld: Library not loaded: /opt/ibmcmp/lib/libxlf90.dylib Referenced from: /usr/local/release1.1/exe/./delphiMacOSX Reason: image not found Trace/BPT trap Does it matter that it's looking for /libxlf90.dylib and I have / libxlf90.A.dylib? Have some xmas charity Help a newb Darren Thompson Graduate Student UCSC 1156 High St. Santa Cruz, CA 95064 831-459-3390 voice 831-459-2395 fax http://people.ucsc.edu/~ministry

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Re: [Chimera-users] Chimera - calculating surface area?
by Elaine Meng 29 Dec '08

29 Dec '08

On Dec 29, 2008, at 8:54 AM, Uli Strych wrote: > Hi Dr. Meng, > I would like to calculate the surface exposed area of only the > hydrophobic amino acid residues for my protein of interest. > I saw your email (at > http://www.ccl.net/cgi-bin/ccl/message-new?2008+03+07+013+raw ) where > you explain how to do so using Chimera. > My problem is the "Attribute Calculator" step, where I don't seem to > be able to find the correct format of entering the formula to > calculate the surface area of the residues that I have previously > selected in the Render/Select menu. Hi Uli, Another necessary step is to show the surface (which creates the surface area values): command "surface" or menu "Actions... Surface... show". You could do that for the whole protein before selecting the residues, or just for the selected residues, either way is fine. That will assign values for the residue attributes named areaSES (solvent-excluded surface area) and areaSAS (solvent- accessible surface area). Then in "Attribute Calculator" you would Calculate attribute [some name, doesn't matter] for [models] Formula: sum(residue.areaSES) with these options checked on: "Restrict formula domain to current selection, if any" (only sum over the selected residues, not all residues) "Open Render/Select by Attribute" (because this dialog will show the answer, the sum value) You want a "models" attribute because you want only one number, the sum over the selected residues. Click Apply (or OK, which would also dismiss the calculator dialog) to calculate the value and show it in the Render/Select by Attribute dialog. Of course, you could use areaSAS instead of areaSES as you prefer. The SES is probe contact and re-entrant surface, and is shown in Chimera. The SAS is where the probe center goes, about 1.4 Angstrom farther out from the molecule, not shown in Chimera. Attribute Calculator manual page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calcula… > This tool is also used in the Attributes tutorial, part 2: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html#p… > I hope this helps! Best regards, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab 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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transparent background error
by odonnell＠chem.fsu.edu 23 Dec '08

23 Dec '08

Hi, I can't find a previous entry in the archives for an error message i receive when i impose a transparent background. As soon as i read in a map i receive this: Runtime error! ProgramC:\Program Files (x86)\Chimera\bin\pythonw.ese R6025 -pure virutal function call Hitting OK I receive... Chimera failed abnormally; the exit code was:255. Thanks in advance for any advice!!!! -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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Still having connection problems with Internet...
by Kenward Vaughan 23 Dec '08

23 Dec '08

Hi all, I wrote in once about this, and have only slowly paid attention to it due to busy schedules, kids, etc. I have build # 2576, and the darned thing pesters me for registration ;-) and still cannot connect for DL'ing PDB's from the data bank. I have no proxy server, and this issue did not exist in earlier versions (I'm uncertain how long ago, to be honest... within a year, I believe). The usual error notice shows up on attempted registration, and fetch attempts give a socket error about a service being unknown: Error reading 1d66: Error during PDB fetch: [Errno socket error] (-2, 'Name or service not known') All other Internet apps I have work well. What else can I try to clear this up? Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

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ubuntu graphics problem
by Elaine Meng 23 Dec '08

23 Dec '08

Fabian reports a Chimera/ubuntu problem and a solution: Begin forwarded message: > > Hi Elaine, > > To save people painful dealing with the newest version of ubuntu, > 8.10, if everybody asks you, chimera has an incompatibility with the > "desktop effects" and "compiz" effects of this version. The only > solution I found (after two days of trials) is to remove compiz (apt- > get remove compiz) and completely disallow the desktop effects > (through system settings). > > Best regards, > Fabian > >> Something more urgent, I have recently updated my kubuntu system to >> 8.10, and the nvidia graphics card to nvidia-glx-177 (177.80 to be >> precise) which should be the correct one. The problem is that after >> a few seconds of working with some molecule in the chimera window >> (which opens fine), it gets stuck and works very very slowly if at >> all. That is a problem since I use chimera very heavily. Any hint >> you could give me of how to solve the problem would be invaluable. >> Just to mention that I have heard of problems with this version of >> kubuntu, but surely there is a workaround. >>

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anti-aliasing in mac version
by Grigore Pintilie 22 Dec '08

22 Dec '08

If I'm not mistaken it looks like anti-aliasing is not used in the mac build of chimera... is there a way to enable this? I'm using a Macbook pro with the nvidia card and Mac os X. Greg

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NMR-Style structures
by Eric Pettersen 19 Dec '08

19 Dec '08

On Dec 18, 2008, at 2:28 PM, Huang, Shengyou wrote: > Is any way for Viewdock in Chimera to open a pdb file with NMR-style > structures so that I can view those NMR-style structures one by one? Yes, you can use ViewDock for that. When ViewDock asks you what the file type is, choose either "Dock 3 or 3.5", "Dock 3.5.x single", or "Dock 4, 5 or 6". Then the normal ViewDock interface will come up. There won't be much information in the various fields because an NMR PDB file doesn't have the embedded information that a DOCK output file does, but nonetheless you can click through the list of structures like normal. Another possibility is to open the NMR file as a trajectory (MD/ Ensemble Analysis->MD Movie) and play through the conformations that way. You could also use other analysis capabilities of the MD Movie tool, such as the RMSD map function. You might also want to try out the Ensemble Cluster tool, which will cluster your NMR ensemble and let you look at representative structures from each cluster. It sounds like you have a lot of conformations, so the Ensemble Match (compare your N structures in an NxN table) and Tile Structures (show all the conformations at once tiled in a grid on the screen) are probably not as useful as they would be for smaller ensembles. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Chimera-users December 2008