April 2009 - Chimera-users - RBVI Mailing Lists

graphics problems, BIOMT, selecting by element, etc.
by Elaine Meng 15 Apr '09

15 Apr '09

On Apr 15, 2009, at 5:30 AM, Cédric Govaerts wrote: > Hi Elaine, Hi Cedric! I will put responses below, after your individual questions... > > I'm not posting my question to the mailing list because most of it > might be > due to my machine. > I've been encountering some problems running chimeras and I suspect a > graphic card issue(s). > Mostly it's the display that goes bananas, lows the machine ending > (sometimes) in a chimera crash. It's OK -- even if due to the machine, other people have these problems too and might want to see the discussion. > > Here are some of the issues : > > 1/ When I zoom in/out using my mouse wheel sometimes all the > displayed atoms > change from wire to CPK representation. I must explicitely change it > back to > wire to go back. > Normal ? > > 2/ When changing the display I have sometimes some very odd graphic > behavior, including part of the window turing colored or black. I > attach a > couple of screenshots. This started just after typing a display > command. For > a while everything became very slow until I tried to save the image > using > chimera itself which seemed to reset the graphics back to normal. > As you can see on the screenshots, some Photoshop tool windows (PS3 > was > running in the backgournd) appear on the image (although not visible > on > chimera itself) which leads me to think that it's a graphics card > issue or a > graphic card+Photoshop issue. These definitely sound like graphics driver issues. Definitely not normal behavior! Things to try are to update your graphics driver as possible, and/or use the Debug Graphics Driver dialog to selectively disable OpenGL features. One way to show this dialog is to go to Preferences (under Favorites), General category, set "debug OpenGL on startup" to true, quit, and restart Chimera. Documentation of the debug dialog and discussion of graphics driver problems: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html > <http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html> > > 1/ Can I easily build a biomolecule from the PDB file ? > I tried with > i) MultiScale Models but could only get low res surfaces > ii) Unit Cell but got the copies from the SMTRY records of the PDB > file, could not specify the BIOMT > I believe the "sym" command should work but I dunno how to make it > read the > BIOMT matrix in the PDB file. > For building using BIOMT: If you use Multiscale Models, you can force loading of the atomic coordinates for all copies by selecting All chains in the multiscale dialog and then changing the Style to anything other than surfaces. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu… > You can also use the "sym" command. If your structure with BIOMT records is model 0, for example, command "sym 0 0": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> > 2/ Is there a way I can select specifically all Mg atoms ? Or - > trickier- all > calcium (Ca) atoms ? commands: select Mg select Ca You can use all the end entries in the Select... Chemistry menu also in the command line. These symbols are in the element submenu. In cases where there is ambiguity, for example H appears both under element and under IDATM type, you can disambiguate like select element.H It will work to use element.Mg and element.Ca ... it's just more typing. > > 3/ When I select with the mouse, I only select one atom at a time. > What > would be the easiest/fastet way to display the residue that the > currently > atom belongs to ? > A/ Can I do it with the command line (does the command line > recognize the manually selected atoms?) ? > B/ I can use the menus and do Actions->Atoms->Backbone->Full and > then Actions->Atoms->Sidechain->Show, but that's a bit cumbersome to > do each > time I wanna see a residue it seems.. If you have some atom or bond in a residue selected, just hit the keyboard up arrow to broaden the selection to the whole residue. That is the same as using the command: select up <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/select.html> You can specify the current selection regardless of how it was created (with mouse, Select menu, etc.) in commands with the word "sel" "selected" or "picked". <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html > For example, pick one atom, hit up arrow, use command "display sel" to display the whole residue. Actually if you use "rlabel sel" (show residue label for any selected atoms) you don't even need the up arrow part. > > That's it for now.. brr, thanks ! > > C > You're welcome! 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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interhelical angle
by Shuanghong Huo 14 Apr '09

14 Apr '09

Dear Chimera Developers, My group needs to calculate the inter-helical angle for a large trajectory. We know Chimera can calculate the inter-helical angle for a conformation. We are wondering what the easiest way to use Chimera to process the whole trajectory. It is amber trajectory. Thanks, Sharon Huo, Ph.D. Associate Prof. of Chemistry & Biochemistry Clark University

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Copy and Pasting sequences
by hsosa＠aecom.yu.edu 14 Apr '09

14 Apr '09

Hi I noticed that in the latest version of Chimera (1.4) the sequence display tool (Model Panel > sequence) is different (nicer looking) than in previous versions. However, before I was able to copy the sequence as text and paste it into a text editor (using CTR-C & CTRL-V in Windows) but that is no longer the case. Is there an easy way to get this functionality back. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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chimera error message
by Michael Zimmermann 10 Apr '09

10 Apr '09

Dear Chimera Staff, I have been trying to learn to use your object model. My goal is to read in an electron density map in CCP4 format downloaded from emdatabank.org and parse out the 3D matrix of electron density values. However, to get started I was trying to just access atomic information in a sample PDB format file (like atomic coordinates). Running through a few of your examples though has proven confusing to me. The following are commands that I have entered into the IDLE. I am using alpha version 1.3 build 2577. >>> import chimera >>> opened = chimera.openModels.open('C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\\ribosome\\70s.pdb') >>> mol = opened[0] >>> from chimera.colorTable import getColorByName >>> red = getColorByName('red') >>> mol.color = red Traceback (most recent call last): File "<pyshell#42>", line 1, in <module> mol.color = red ValueError: underlying C++ Molecule object is missing Why is there a module missing? How do I find out what module is missing and add it? >>> red.name <built-in method name of _chimera.MaterialColor object at 0x0F1AAF38> >>> red.rgba <built-in method rgba of _chimera.MaterialColor object at 0x0F1AAF38> What if I want the value displayed rather than the object's ID? Is there a get method that has to be invoked? What would the syntax be? >>> ATOMS = mol.atoms Traceback (most recent call last): File "<pyshell#54>", line 1, in <module> ATOMS = mol.atoms ValueError: underlying C++ Molecule object is missing Again, why is a module missing, how do I find out what module is missing, and how do I add it? Thank you, Michael Z

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reading complex-float mrc files
by Benoit Zuber 10 Apr '09

10 Apr '09

Hi, I was wondering if it is possible to read mrc files where the data type is complex float. I get an error when I try to do that, but maybe there is a way around it (other than converting the data to a non complex type). Typically, this would be useful to read fourier transform volumes. Thanks, 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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deleting arrows
by Bala subramanian 10 Apr '09

10 Apr '09

Dear Chimerians, I created one .bild file and loaded it in chimera. When i use del command the object is not getting deleted. open eg.bild del #0 -> now the arrows that are displayed on the screen is not deleted. Why is it so ? Thanks, Bala

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Renaming chains in "combine" command
by Fajer 10 Apr '09

10 Apr '09

Hi, I am a complete newbie to chimera. I have added a loop sequences to using addaa but the new loop has a different chain designation from the rest of the molecule. "Combine" command preserved the differences in chain id. How can I make the new loop chain to be the same id as the host ? peter

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question
by Tatyana Fedotova 09 Apr '09

09 Apr '09

Dear Mrs/Sir, My name is Tatyana and I am new to Chimera. I hope that you can help me with my question. I have opened pdb file with DNA and protein coordinates. I would like to mutate some residues and base pairs. Do you know how I can introduce them? Thank you, Sincerely, Tanya Tatyana Fedotova, Dpt. of Biochemistry & Molecular Biology SUNY Upstate Medical University 750 East Adams Street Syracuse, NY 13210 Cell: 404-386-5950 Office: (315) 464-8734 Fax: (315) 464-8750

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Re: [Chimera-users] chimera difference map
by Eric Pettersen 09 Apr '09

09 Apr '09

On Apr 9, 2009, at 9:23 AM, Negi, Surendra S. wrote: > > Hi Eric, > > I have a quick question related to chimera. Can we use chimera to > calculate the difference map between two EM densities. Hi Surendra, I don't know the answer to this off the top of my head, so I'm cc'ing this to chimera-users, where someone who does know the answer can reply. --Eric

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Modification of b-factor and occupancy
by Tom Goddard 08 Apr '09

08 Apr '09

Tsutomu Matsui wrote: > Hi Tom, > > Is it possible to change b-factor or occupancy of selected atoms, and > then output the coordinates including those changes? > > Tsutomu > Hi Tsutomu, Here are Chimera commands to set bfactor and occupancy of an atom (model #0, residue 13, chain B, atom CA) and write out the PDB: setattr a bfactor 12.3 #0:13.B@CA setattr a occupancy 0.123 #0:13.B@CA write 0 /tmp/test.pdb If you really mean you want change the "selected" atoms use a command like: setattr a bfactor 12.3 sel See the setattr and write documentation for more details. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html Tom

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Chimera-users April 2009