August 2008 - Chimera-users - RBVI Mailing Lists

electrostatic surface coloring
by James Fethiere 22 Aug '08

22 Aug '08

Hi, 1. is there a way to use the electrostatic surface coloring from the tools/surface menu, in a command file? It seems that it is only available through the menu? 2. I have a pqr electrostatic potential file calculated from the PCE server http://bioserv.rpbs.jussieu.fr/Help/PCE.html using MEAD. How do I get it into chimera? Thanks

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Dr. Simon Sauve is out of the office.
by Simon Sauve 22 Aug '08

22 Aug '08

I will be out of the office starting 2008-08-21 and will not return until 2008-09-03. You can reach me at simsauve(a)yahoo.ca during the ICMRBS conference. In case of an emergency, please contact Dr. Yves Aubin by e-mail or @ 613-941-6155

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emulation of threee button mouse not working
by Geeta Narlikar 22 Aug '08

22 Aug '08

Hi, I'm having problems with the three button mouse emulation feature. My OS is Mac X Leopard and I turned on the "emulate three button" mouse feature in X11. But that does not seem to work. My version of Chimera is 1.2509. Is there any other setting I should change? Thanks for your help. Geeta Narlikar

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Re: [Chimera-users] density maps in chimera- question
by Thomas Goddard 21 Aug '08

21 Aug '08

Hi Sarah, You can use the keyboard shortcut "bv" to create a new map that covers your PDB model. To enable keyboard shortcuts use Tools / General Controls / Keyboard Shortcuts and turn on "Enable keyboard shortcuts" in the dialog. Select the atoms of your PDB model. If you have more than one map open make sure the highlighted one in the volume dialog is the crystal map for the selected atoms. Then type the "bv" shortcut to create a new map covering the select atoms. This assumes that the starting map is a full unit cell. If you don't want to go to the trouble of enabling keyboard shortcuts, you can use the command "ac bv" which runs the shortcut (accelerator) bv. You can save the covering map with volume dialog File / Save Map As.... Tom Sarah Boyce wrote: > Hi Tom- I was told you might be the person to ask about the density map > features in chimera. I'm trying to display crystallographic electron > density maps and I've run into a problem aligning some of the maps to > the protein model. When I load the map and model it looks as though the > map is of the symmetry related molecule, but when viewed using Coot it > automatically centers the map on the model. So far the only tool that > I've found to do this is by hand alignment, which doesn't work at all > for an atomic level model (or at least when I've tried it it is too much > of a pain). Is there an automated tool in chimera that will > automatically center the map on the model similar to the way Coot > handles it? > > > Thanks, Sarah

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(no subject)
by charles marchand 21 Aug '08

21 Aug '08

Greetings, I was wondering if someone could tell me how to select multiple sequences in the sequence viewer. I am trying to select different regions of RNA to visualize, but Chimera has not allowed me to pick to sequences that are separate. Is there a way to do it through the sequence viewer? Thank you, Charlie

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Re: [Chimera-users] CHARMM PBEQ calculations
by Tom Goddard 21 Aug '08

21 Aug '08

Hi Fabian, The OpenDX file you sent has a small but important error. It is missing the words "data follows" at the end of the header line that says "object 3 class array..." so Chimera never reads the data. The misleading error message comes about because the last line of the file is blank and Chimera still thinks it is reading the header. The header line object 3 class array type double rank 0 items 378885 has to be object 3 class array type double rank 0 items 378885 data follows Hopefully Sunhwan can update the phi2dx.py script to include the very important "data follows". The OpenDX format is described in Appendix B of the OpenDX User's Guide: http://opendx.npaci.edu/docs/pdf/userguide.pdf Tom Fabian Glaser wrote: > Dear Elaine, > > I am afraid it's still giving the same error when I try to open the dx > file, even when the first line is removed or # starts it. Here is the > message: > > Opening /media/data/WORKSPACE/PROJECTS/DanCassel/COP/step2_pbeq.dx > Error reading file step2_pbeq.dx, format apbs > Incorrect format: blank header line. Comments must begin with # > character. > > And the dx file is attached, probably I am doing something wrong.... > > THanks a lot, > > Fabian > > > Elaine Meng said the following on 19/08/08 19:19: >> Hi Fabian, >> Well, the error message says the format is wrong. Based on the >> message, you could try removing the blank line at the top of the file >> or adding # in front of it. >> >> If that still doesn't work you could send me the file to look at, but >> it is probably just a simple fix such as the above. >> 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 19, 2008, at 7:03 AM, Fabian Glaser wrote: >> >>> Dear Sunhwan >>> >>> Thanks a lot for your kind answer and for the script. The script run >>> fine, but when I try to upload it to chimera I get an error: >>> >>> Opening >>> /media/data/WORKSPACE/PROJECTS/HaimManor/EladEliahoo/MODELS/POMBE/CHARMM-PBEQ/charmm-gui/step2_pbeq.dx >>> >>> Error reading file step2_pbeq.dx, format apbs >>> Incorrect format: blank header line. Comments must begin with # >>> character. >>> Done opening >>> /media/data/WORKSPACE/PROJECTS/HaimManor/EladEliahoo/MODELS/POMBE/CHARMM-PBEQ/charmm-gui/step2_pbeq.dx >>> >>> >>> Which maybe perfectly chimera problem, so I am CCing this email also >>> to Elaine Meng from the CHIMERA team. >>> >>> Any help will be very appreciated, >>> >>> Thanks a lot, >>> >>> FAbian >>> >>> Sunhwan Jo said the following on 19/08/08 15:25: >>>> Dear Dr. Glaser, >>>> >>>> I'm afraid CHIMERA is not able to read CHARMM phi80 format. But simple >>>> search guided me that CHIMERA can to read dx format file, which I >>>> have a >>>> converting script. So, please find the script in the attached file. >>>> We've been >>>> using this script to read our potential data in Pymol, so I believe >>>> this should >>>> be working fine with CHIMERA as well. >>>> >>>> usage: >>>> python phi2dx.py step2_pbeq.phi80 > step2_pbeq.dx >>>> >>>> Please feel free to contact me, if you have a further problem. >>>> >>>> Thanks, >>>> Sunhwan >>>> >>>> >>>> On Tue, Aug 19, 2008 at 4:53 AM, Fabian Glaser >>>> <fglaser(a)technion.ac.il> wrote: >>>> >>>>> Dearl CHARMM team, >>>>> >>>>> have been trying to upload the electrostatic potential calculated >>>>> by CHARMM PBEQ routine to the CHIMERA viewer, since the java >>>>> viewer you use is very good but at least in my machine does not >>>>> work. But despite I have been trying to upload it to chimera there >>>>> seems to be some stubborn problem (or I am doing something wrong). >>>>> What I am trying to do is to color the pdb by the potential in >>>>> chimera so I can freely manipulate it and compare it with other >>>>> calculations. >>>>> >>>>> If you have any suggestion I'll be very grateful, >>>>> >>>>> Best regards, >>>>> >>>>> Fabian Glaser, PhD

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clipping planes question
by William Jeffrey Triffo 20 Aug '08

20 Aug '08

I know of the hinder and yon clipping planes, and also the per-model clipping plane that allows individual model clipping. I have a current imaging session where I have already used per-model clipping on several models, but would like to trim off some material from the side of the entire combined model - I don't suppose there is an arbitrary clipping plane that applies to the whole scene, like hinder-yon but from any user-defined direction? For now, I was just going to crop the resulting image. But this will result in an abrupt end to the background color (I can adjust the image border clone the background in photoshop/etc, but would be nice to be able to do that within Chimera) thanks, -Jeff

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saving nol2 files
by 吴超 20 Aug '08

20 Aug '08

Hi, dear folks, I have some doubt about how chimera determines the atom type when you save mol2 files from ligand pdb files. Because when I opened the saved mol2 files, I found there were some mistakes about atom type. Does Chimera use the same procedure that Sybyl uses to determine the atom type? -- Chao Wu

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MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ???
by Darrell Hurt 20 Aug '08

20 Aug '08

Hi there, I¹m trying to use the command MultiScale.color_surfaces_to_match_atoms(). I want to point out a mutation on the surface of a virus. I can color the atoms correctly, but I can¹t figure out how to apply that color to the MultiScale low-resolution surface. Any hints on how to use this command? Also, how can I increase the mesh resolution on MultiScale surfaces for input for 3D printing? Thanks! Darrell -- NIH Researchers: check out our new web site <http://inside.niaid.nih.gov/topic/IT/bioinformatics/Pages/default.aspx> Darrell Hurt, Ph.D. Section Head, Biocomputing Research Consulting Bioinformatics and Scientific IT Program (BSIP) NIAID Office of Technology Information Systems (OTIS) National Institutes of Health, DHHS Contractor, Lockheed Martin 4 Memorial Drive, Room 424 Bethesda, MD 20892-0485 Mobile: (301) 758-3559 Fax: (301) 402-0366 NIAID Intranet: http://bioinformatics.niaid.nih.gov <http://bioinformatics.niaid.nih.gov/> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Re: [Chimera-users] Distance and Angles
by Thomas Goddard 20 Aug '08

20 Aug '08

Hi Andy, To show a distance between atoms select the two atoms and use menu entry Tools / Structure Measurements / Distances and press the Create button. You can show distances for multiple pairs of atoms. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… Not sure what you mean by the angle between two density map surfaces. The surfaces intersect in many places making different angles. You could place 3 markers with Volume tracer and measure the angle made by those 3 markers using the Angles/Torsions tab of the Structure Measurement dialog. Tom Anindito Sen wrote: > Hi Tom > > Probably this question is already answered before- > > How do I show multiple distances between different amino acids of two > molecules from two different parts of the density map. > > Also do can I determine the angle between two surfaces? > > Thanks > Andy > > Dr. Anindito Sen (Ph.D) > Research Associate , Dept. of Biochemistry and Molecular Genetics > University of Virginia > Box 800733 Charlottesville, VA 22908

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