October 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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using EMAN/AIRS/SSEHunter
by Peter Hildebrand 10 Dec '08

10 Dec '08

Hallo there, we have installed the AIRS (EMAN 1.8) Package for Chimera (build 2470), but have difficulties to get it run. steps to reproduce: launch Chimera load .mrc file calling tools/AIRS/SSEHunter there is no file to select in the 'MRC file' selection box. If we provide parameters for Angstrom, Resolution and threshold and press 'Apply' we get this: ================================================================= UnboundLocalError Exception in Tk callback Function: <function command at 0x89f67d4> (type: <type 'function'>) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/chimera/baseDialog.py", line 238, in command None File "/usr/local/EMAN/chimeraext/Airs/ssehunter.py", line 89, in Apply targetPath=airsIO.getPath(target) File "/usr/local/EMAN/chimeraext/Airs/airsIO.py", line 62, in getPath return path UnboundLocalError: local variable 'path' referenced before assignment ================================================================= Are we using this module in the wrong way (wrong parameters e.g.) or is it a bug (where?). Thanks in advance, jan and peter

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Fwd: Combining fragments for RESP charges
by Francesco Pietra 31 Oct '08

31 Oct '08

Sorry I used the wrong address for the message below. ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Fri, Oct 31, 2008 at 8:34 AM Subject: Combining fragments for RESP charges To: chimera-users-request(a)cgl.ucsf.edu I was reading Ross Walker's tutorial A1, in the suite of tutorials for Amber. When deriving RESP charges for an unusual molecule covalently bound to a protein, the unusual molecule is first detached from the protein and then further divided into fragments. RESP charges are derived for the fragments, then the fragments are recombined using Sirius visualization program. The recombined fragments are then attached to the protein, again using Sirius. Can these recombinations be carried out with Chimera? Thanks francesco pietra

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morph-coordinates and camera movements
by Matthew Dougherty 30 Oct '08

30 Oct '08

I was generating a morph of atoms and wanted to rotate the camera 242 degrees on the x axis. I am thinking there may be several ways to do this, such as per-frame script in the morph tool or through the movie recorder script. Is one way better than the other? What would the scripts look like? Thanks, Matt

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directory within Chimera ??
by Barry Lever 30 Oct '08

30 Oct '08

Elaine: I know you are busy .. but as a fairly new user....when I restore a previous session.. can I extract from Chimera, the names of the input data files that were used to create that molecule and subsequent manipulations- I am especially interested to know where I can locate the name of the input geometry file that set up the molecule. In future I will know to include that information in the overall session file name but for now..... Thanks so much Barry -- A. B. P. Lever Distinguished Research Professor Emeritus Chemistry, CB124, York University 4700 Keele St., Toronto, Ont., Canada M3J 1P3 Tel:416-736-2100 x22309 Fax: 416-736-5936 http://www.chem.yorku.ca/profs/lever

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multiple Chimera windows on Mac
by Elaine Meng 30 Oct '08

30 Oct '08

On Oct 30, 2008, at 8:07 AM, Chin-Hsien (Emily) Tai wrote: > > One quick question, is there any way to have several sessions of > Chimera running at the same time so that we can compare/rotate > different domain parsing results of the same structure at the same > time? > Hi Emily, I assume you are using a Mac... Yes, you can have multiple Chimera instances, as many as you want, if you start Chimera from the Terminal window. For example, I have Chimera version 1.2540 installed as /Applications/Chimera2540, so to start it from Terminal I would type: /Applications/Chimera2540.app/Contents/MacOS/chimera Actually I don't really type that because it is too troublesome, and instead have an alias in my home directory .tcshrc file (or .cshrc file). If you don't have either of these files you can just create a file by that name in your home directory and put the alias in it, in my case: alias chimera /Applications/Chimera2540.app/Contents/MacOS/chimera Then after you source that file or log in again, simply typing "chimera" (or whatever you used as the alias) starts Chimera. In a second Terminal window, you can enter "chimera" for a second running Chimera, etc. I have multiple different Chimera versions with different aliases, for example, a recent daily build is on my Desktop: alias chinew ~/Desktop/Chimera.app/Contents/MacOS/chimera Even if you have only one version, you can start it as many times as you want from different Terminal windows. I hope this helps, 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

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scripts in Chimera
by Ben Keshet 29 Oct '08

29 Oct '08

Hi, I am reviewing a large number of structures (docking results). I uses the ViewDock tool which is great and makes life much easier. Still, for every file I open with ViewDock, I repeat the same set of commands before actually reviewing the poses, that is (initially only the receptor structure is open, with only ribbon shown): 1. open the ligands mol2 file. 2. color by element 3. choose atoms within 6A from the ligands (by selecting the ligand, than select zone<6A). 4. show the selected atoms. This is to show only receptor atoms within 6A of the ligand. Is there a way I can "record" this sequence or write some simple script that I could run after opening the ligands mol2 file? Thanks! Ben

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volume planes display loop
by Benoit Zuber 28 Oct '08

28 Oct '08

Hi, I have got some questions regarding plane display of volumes: Is there a way to cycle through a limited range of planes? For example if the thickness of my volume is 300, is it possible to cycle from z = 100 to z = 120, instead of from z = 0 to z = 299? Is there a way to make the cycling through the planes start in the other direction than when it stopped last time? For example, I click stop while the display is cycling from low z value to high z value. If I then click start, the display is going to cycle again from low to high z value but I would like it to cycle from high to low z value. Is it possible to specify a starting plane and an end plane, and to have the display going from the starting plane to the end plane only once (without cycling)? Finally, can all of this be specified through the command line? Cheers, Ben Benoît Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber(a)mrc-lmb.cam.ac.uk

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Flushing output during the script execution
by Lukas Palatinus 27 Oct '08

27 Oct '08

Hello all, I am using Chimera as a visualization tool for small-molecule electron densities obtained by ab initio structure solution. I want to create a small script that will make Chimera read and display the intermediate electron densities as they are produced during the iterative structure solution process. I am not skilled in Python, but I could make a simple Python script by copying and modifying scripts previously posted in this list. Here is the script: from chimera import runCommand as run from os.path import exists from time import sleep map_file= 'test.xplor' while exists(map_file): run('close all') run('open ' + map_file) sleep(1) I am sure this is not the most elegant way to achieve what I need, but it should do the job. What the script should in my opinion do is to read and display the file test.xplor, then wait one second, close the map and reopen it again, until the file test.xplor is deleted. The script does >>almost<< that, it opens the volume viewer, reads the map, but it does not display the map in the main Chimera window. Only after the file test.xplor is deleted, the last map is displayed. Can anybody give me a hint what am I doing wrong? I am using Chimera 1.2540 on Mac OS X 10.4. Thanks in advance for any help. Best regards Lukas Lukas Palatinus Laboratoire de Cristallographie EPFL Lausanne Tel.: +41 (0)21 693 0639 mailto: palat(a)fzu.cz

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Chimera-users October 2008