May 2008 - Chimera-users - RBVI Mailing Lists

Renaming chains in a PDB file with two chains
by Harinathachari Bahudhanapati 10 May '08

10 May '08

Hi Elaine, Thanks for all the answers you give to our questions. They are very helpful as I learn more everyday. I have a question. Is there anyway to rename a chain in a PDB file through the GUI? I have a few PATCHDOCK generated PDB files with two different chains named under Chain 'A' as #0.1 and #0.2. When I try to get the list of hydrogen bonds between these two chains, the chain name 'A' appears for all of the h-bonding pairs. So, I want to have them named Chain A and Chain B for easier analysis than scratching my head figuring out which h-bond pair is between the chains or with in the chain. I am attaching the pdb file. Please help me. (I thought of renaming the chains in the PDB file going through the PDB header (text file) and manually changing the name. But I am not a expert if anything goes wrong.) Sincerely Hari

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Dashed H-bond
by Ibrahim Moustafa 10 May '08

10 May '08

Dear Chimera Team, Few weeks ago I asked about how to make H-bonds with dashed line style, I got your great help in that. So, I can make the H-bond with the color and style I want; however, when saving the image (with POV true) I got the H-bond appeared with the new chosen color but not as dashed line shown in the display. But, if I save the image with POVray option false, I got the same style shown in the display (new color and dashed line). The question is why saving the image using ³POV true² does not give the image as it appears in the display? Again, it accepts the new color but not the dashed style. Thanks for your great help, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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Number of voxels?
by Kolodziej, Steven J 09 May '08

09 May '08

I was wondering if anyone knows how to tell how many voxels within a bounding box can be assigned to protein signal instead of "empty space" at any given contour/density level? Thanks, Steve Kolodziej

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saving a stereo image
by Elaine Meng 09 May '08

09 May '08

On May 9, 2008, at 9:04 AM, Pallan, Pradeep S wrote: > > Hi Elaine, > I am trying to save a generate a stereo image by following the > instructions: > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ > frameimages.html > > I captured left eye and right eye images separately, pasted > them side by side ~65 mm apart, and I see this do not appear as > stereo. Any comments and instructions? I can send you the image > if you want to take a look at it. > > Thank you very much, > Pradeep Pallan Hi Pradeep, I think you are looking at old documentation. I don't think the current documentation says anything about saving separate images for left eye and right eye. This is the current page: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/ print.html#stereo Here is the blurb from that page, but it is probably better to go to the URL because there are helpful hyperlinks: Stereo. Wall-eye, cross-eye, and red-cyan stereo images can be saved by changing the graphics window to the corresponding camera mode with the Camera tool (or the command stereo) and using the "same as screen" Image camera mode in the Save Image dialog. Another way to save cross-eye stereo images is with the "stereo pair" Image camera mode; in that case, it does not matter what camera mode is being used in the graphics window, but the resulting image will be twice as wide as the specified size. Those approaches should work, assuming you also have a recent version of Chimera! (last production release Nov 2007 or newer) Best, 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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Selected residues already shown on the screen
by Ibrahim Moustafa 08 May '08

08 May '08

Dear Chimera team, How to include residues previously selected and shown on the screen with a new selection? For example, I did a selection for few residues and displayed them on the screen; then removed the selection. I wanted to run hbond on those residues already on display. How to do that? Thanks, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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MemoryError restoring session
by Eric Pettersen 07 May '08

07 May '08

Christian Rickert wrote: > At the university, I saved a huge project of mine containing a > density map and multiple (!) rigid-body fitted pdbs. > Although this system is a 32-bit Kubuntu 8.04 only (4 Gig of RAM > installed), I observed the same problems with my 64-bit SUSE 10.3 > (4 Gig of RAM installed as well) at work. > > Creating this project took me two days in total, so I really would > appreciate any suggestions from you ... Hi Christian, It's possible that your shell is imposing a limit on memory use by a single process. Before starting Chimera, remove the memory limit of your shell by typing: csh-type shell: unlimit sh-type shell: ulimit -v unlimited Let me know if this helps or not. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to use hbonds spec
by Miguel Ortiz-Lombardía 07 May '08

07 May '08

Hello, I'm trying to follow hydrogen bonds in a trajectory from amber. To do so, I would like to run a 'per frame' script with something like: hbonds spec :100 selRestrict cross relax false However, this fails because apparently no atoms are selected. This fails as well: hbonds spec #0:100 selRestrict cross relax false I can only see the hydrogen bonds if insert a select :100 before the hbonds command. I wouldn't like to see the green 'aura' of the selection, that's why I would like to make the selection within the hbonds command. I'm probably missing something, but cannot figure out what. Thank you! Miguel -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

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Tile structure request
by Eduardo Sanz-Garcia 07 May '08

07 May '08

I noticed that the tile structure option arranges the models logically when there are 5 or less models opened. When there are 6 or more, the arrangement is a little bit chaotic, the models are not placed sequentially. Could this option be improved so the sequence is more logical? Thank you very much. Chimera is great!! PS: I am used to work with EM models, I don't know if the previously described behaviour also applies to atomic coordinates models.

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solvent-accessible surface area
by Elaine Meng 06 May '08

06 May '08

Dear Jose, Prof. Ferrin forwarded your question to me. Our program Chimera, the successor to MidasPlus, can calculate the solvent-accessible surface area. It is available for download for Windows, Mac OSX, Linux and other platforms. The features I will mention are relatively new, so you would need to get a recent version such as the May 1 snapshot: http://www.cgl.ucsf.edu/chimera/download.html#snapshots You would first load the structure in Chimera (File... Open for a local file, File... Fetch by ID to get it directly from the PDB). Then there are a couple of different approaches you could take. (1) simply show a molecular surface in Chimera (Actions... Surface... show) or command "surface". The total will be reported in the Reply Log (under Favorites in the menu). You can use the solvent- accessible value or solvent-excluded as you prefer. The difference is explained here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ representation.html#surfaces Besides the total, the values per atom and per residue are assigned as "attributes" named areaSAS and areaSES for solvent-accessible and solvent-excluded, respectively. You can see a histogram of the values by opening "Render by Attribute" (under Tools... Depiction), and you can write out the values to a file by choosing File... Save Attributes from that dialog's menu. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#render The Render dialog can be set to show the values for "atoms" or "residues" (simply the sum over the atoms in each residue). What it writes out are the atom (or residue) specifiers and the value for each, not a grid. (2) instead of doing the calculation in Chimera, you can send the coordinates to a web server with the tool "Area/Volume from Web" (under Tools... Surface/Binding Analysis). There are various options for what you want to calculate. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html Again you get the values assigned as attributes (but this time atoms only) and can view and save them in the same way as described for #1 above. The help links above are part of the User's Guide, which is also accessible from the Help menu of Chimera, once you have downloaded it (Help... User's Guide, Search Documentation, Tutorials). If you still have trouble you can send questions to chimera-users(a)cgl.ucsf.edu I hope this helps, 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 On May 5, 2008, at 4:52 PM, Tom Ferrin wrote: > ------- Forwarded Message > > Date: Wed, 30 Apr 2008 17:20:27 -0400 > From: Jose Gascon <jose.gascon(a)uconn.edu> > To: tef(a)cgl.ucsf.edu > Subject: midasplus > > Dear Prof. Ferrin > > I am an Assistant Professor in the Chemistry Department at UConn, I am > interested in calculating the solvent accessible area of a protein. I > looked up on the internet and found that the program midasplus is > suppose to do that. The links seem to be outdated and I was not been > able to find the program. I assume that midasplus has probably evolved > to other programs such as chimera. I understand that you were involved > in the development of this program. > > At the end, given a pdb input file, I am just interested in > obtaining a > grid of x,y,z coordinates representing the SAS. > Do you know if there is such a program? Is DMS, from midasplus, still > available somewhere? > > Thanks for your help. > > Sincerely, > > Jose A. Gascon > > > -- > Jose A. Gascon - Assistant Professor > 55 North Eagleville Rd. > Department of Chemistry > University of Connecticut - (860) 486-0591 > Storrs, CT 06269 > http://gascon.chem.uconn.edu > > ------- End of Forwarded Message >

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movie trajectory
by Jean-Paul Armache 06 May '08

06 May '08

Hi Elaine, Eric, Thanks for the answer - I know the webpage for the movies, but it will be helpful to use the savepos command. I will let you know whether this produces the desired effect or further help will be needed. Best regards, Jean-Paul

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Chimera-users May 2008