August 2008 - Chimera-users - RBVI Mailing Lists

POV-ray ignoring surface clipping
by Monica Tello 31 Aug '08

31 Aug '08

I am having trouble saving my images when they have a surface clipped to show the inside. If I have a surface around my ligand and is partially clipped, at the time of saving the image: - If I save it without using POV-ray, it saves the exact same view as on the screen, with the surface clipped. - If I use POV-ray, it saves it with the full surface around the ligand, ignoring the clipping I had done. I have tried modifying several POV-ray settings but nothing has worked! Have you got any suggestions? Thanks! Monica ------------------------------------------------- Monica Tello Soto, PhD The Salk Institute for Biological Studies Chemical Biology and Proteomics 10010 North Torrey Pines Road San Diego CA92037 858 453 4100 x1946 tello(a)salk.edu ------------------------------------------------

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automating/scripting bond rotation
by E. Merkley 29 Aug '08

29 Aug '08

Hello chimera team, I am trying to evaluate which regions of (chi1,chi2) space for a particular tryptophan residue create steric clashes with a bound ligand. I see from the archives that findclash can be called from the command line, but I have been unable to find a way to use the "adjust torsions" feature from the command line. Is this possible? If not, any other suggestions? Thanks in advance, Eric Merkley

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decommissioning SGI Irix platform
by Eric Pettersen 29 Aug '08

29 Aug '08

Hi all, We are decommissioning our SGI machines as of 9/15, which means that the 1.2540 release was the last production release for SGI Irix. Daily builds will continue to be made for SGI until 9/15, so some post-1.2450 fixes/features will be available that way. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Povray and semitransparent maps
by odonnell＠chem.fsu.edu 29 Aug '08

29 Aug '08

Hi. I'm seeking a tip or two on how to save an image of a semitransparent map with PovRay. Povray works fine, but the image of the semitransparent map it generates is much darker that it appears on the screen. Any advice would be much appreciated. -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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ESP surface, DelphiController
by Elaine Meng 28 Aug '08

28 Aug '08

Hi James, Just because it has red, white and blue blotches does not mean it is showing ESP!! I don't think the different filenames in the DelPhi log are a problem - I believe temp files are generated from the ones you specify and used in the calculation for technical reasons. However, I do not know the reason for the error and not getting any output. You could try using Help... Report a Bug in the Chimera menu - give more details, such as all the error messages obtained and what it says at the end of the DelPhi log file. The main difficulty with DelPhi and any ESP calculation program is that atom names need to match those in the DelPhi charge parameter files. If you want to use all the hydrogens, you have to either edit all the names in the DelPhi charge parameter file or write out your PDB beforehand and edit all of its atom names to match those in the DelPhi charge parameter file. I have found this to be well nigh impossible. In general many hydrogen names not match and your molecule gets a very large net negative charge. Chimera tries to name hydrogens according to current PDB standards, but these old DelPhi parameter files use a different set of names. Instead, I would just used the DelPhi parameter files "default.crg" and "default.siz" which ignore hydrogens and just plop positives on nonhydrogen atoms in Lys, Arg (maybe His and N-term, I forget) and negatives on nonhydrogen atoms in Asp, Glu (maybe C-term). It is impossible to tell what "half all red" and "half all blue" means. It depends on what levels you have specified to be displayed as red and blue. Maybe the APBS map is fine - try changing the values set to red and blue to larger magnitudes. If APBS writes some sort of log file I would look at that, see if there is a reasonable net charge. Again most of the trickiness is in getting the right charges assigned to the atoms. You could use the PDB2PQR server to get an input file for APBS (if you didn't try that already). <http://nbcr.sdsc.edu/pdb2pqr/> Another possibility is to use the webPIPSA server as mentioned in previous messages, e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/003006.html Best, 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 On Aug 27, 2008, at 7:58 PM, James Fethiere wrote: > Hi Elaine, > > Nice that you found what I did 6kkm away!!! thanks. However, I must > say that it does look artificial. I'm just desperate to get the > electrostatic look as nice as possible (just like the pictures in http://www.cgl.ucsf.edu/chimera/tutorials/maps08/exercises.html#esp) > and found that was the closest I could get. One example I'm trying > is on 1DH3 > > On this note, I did try the delphicontroller to get the true > potentials but cannot get it to work. I have installed delphi on > windows-XP and called it from within chimera with tool/ > surfaceanalysis/delphicontroller. I entered the path for the > executable and charge and radii files. When I run delphi, I get an > error with no output file generated and some strange parameters in > the log file: > > in(pdb, file="tmph4vkzc") This does not correspond to the chimera > model I have chosen > in(siz, file="tmplk_go0") same here; not the file specified > in(crg, file="tmpbg7nlz") same thing > AC = true > CS = true > PF = 60 > SC = 1.2 > PR = 1.4 > FC = true > LG = false > LP = false > PX = false > PY = false > PZ = false > BC = 4 > ID = 2 > ED = 80 > GC = 0.0 > IS = 0.0 > IR = 0.0 > NI = 0 > > P.S. I did addH before starting Delphi! Any idea of what is going > wrong? > > I also tried to run APBS and got a potential file. But when I read > it in chimera, I get strange looking surfaces with half all red and > half all blue!!! here again I could use some guidance. > > Thanks for your help. > > James > -- > James Fethiere, Ph.D. > Institut de Recherche en Immunologie et Cancerologie > Pavillon Marcelle Coutu, University de Montreal > 2900 edouard-montpetit > Montreal, Qc H3t 1J4 > Tel: 514-343-6111 ext. 0918/0919 > Fax: 514-343-5839 > james.fethiere(a)umontreal.ca

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unattended installation on Windows
by Nelson, Lisa 27 Aug '08

27 Aug '08

Hello, I am not a chimera user; I'm an IT person. I have been asked to provide this application for next semester on our walk-up Windows computers for students. I have downloaded the necessary Windows installation materials, but I cannot find any documentation about command line parameters for the installation process itself, and the installation executable does not appear to be one of the usual suspects that I'm familiar with. Specifically, I'm looking for a way to do unattended, silent installation from a batch file. Attended installation is not an option as there are thousands of computers involved. Thanks for any help anybody can provide. I am not on the chimera mailing list, so please send replies privately. (The "contact us" webpage appears to give me the option of e-mailing to this list even though I'm not a member, so since I have only this one question and no particular need to subscribe, I've done it this way.) Thanks, Lisa.

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selection
by James Fethiere 26 Aug '08

26 Aug '08

Hi, I'm trying to create a category for separate surfacing of chains in a session that has multiple models. The following command: _surfcat sh3 #7:.a, surf sh3_ returns mangled atoms specifier. This may looks trivial but I can't find the right syntax to specify both the chain and residues in the same command. Any idea? Thanks James

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mrc opaque faces
by Benoit Zuber 26 Aug '08

26 Aug '08

Hello, I have problem looking at maps in mrc format calculated with IMOD. In mesh or surface style, when I move "level" towards lower value, the outer faces of the volume gradually become opaque. When I set the level to the minimum I see a smooth rectangular parallelepiped. I can then zoom in and have the camera inside the parallelepiped. With these settings, no density is visible inside the parallelepiped, only its faces are visible. In 3dmod I checked the edges of the map: they have a variable density, and they are not all black, or all white. Has anybody got a clue of what's going wrong? Thanks Ben -- Benoit Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK

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Faster volume plane display
by Thomas Goddard 25 Aug '08

25 Aug '08

Optimization for tomogram display. I optimized volume plane display making flipping through size 2048^2 data planes run at 17 frames per second instead of the 1.2 frames per second in the last Chimera production release 1.2540. This is with solid style rendering (gray-scale) and with mid-range graphics cards (tested on Radeon X1600 and Radeon 9800 Pro). The improved performance will be available in tonights Chimera daily builds. http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom

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Re: [Chimera-users] density maps in chimera- question
by Tom Goddard 22 Aug '08

22 Aug '08

Hi Sarah, Chimera does not show sigma values for a crystal map in the volume dialog. It shows whatever values are actually in the map file. Here is a description of how to convert to sigma values: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html Chimera map display was primarily intended for electron microscopy, hence the deficiencies with crystal maps you are encountering. Allowing direct display of sigma values is item 153 on our requested features list: http://www.cgl.ucsf.edu/chimera/plans.html Tom Sarah Boyce wrote: > Thanks Tom. I also was wondering about the display options for the > density. How does the histogram display level correlate to the sigma > level of the map? > > Sarah

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Chimera-users August 2008