- Chimera-users - RBVI Mailing Lists

Calc buried surface area between 2 chains
by Tom Duncan 30 Jan '09

30 Jan '09

I saw an earlier post (Dec. 29, 2008; Digest vol. 68, issue 28) in which Elaine Meng described a procedure for calculating surface area for selected atoms. I did this for atoms on chain A that were selected as contacting atoms on neighboring chain B, but the sum(atom.areaSES) probably includes area buried within the chain A, not just between the 2 chains. I tried checking this by calculating the sum(atom.areaSES) for chain A (all atoms in A) in the whole model, then again for a model from which chain B was deleted before calculating the surface. However, the results indicated a larger areaSES for chain A in the absence of chain B! There were some errors reported in calculating the surfaces; perhaps this contributed. Is there a better way to calculate the buried surface on 1 chain due to contacts with a 2nd chain? Thanks, Tom Duncan

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error message
by Katherine Parra 28 Jan '09

28 Jan '09

Hello! I'm trying to get the hydrogen bonds between some selected residues during a trajectory, using per frame commands from tools. But when I get the possible hydrogen bonds formed between the selected residues I also get the following error message in the Reply Log: *Skipping possible acceptor with bad geometry: #0:2108@O Wrong number of grandchild atoms for phi/psi acceptor #0:2108@O *What could be happening? Thank you in advance. KP

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color zone on command line
by Giulia Zanetti 28 Jan '09

28 Jan '09

Hi all, I would like to make a movie in which areas of my map are coloured while the surface is rotating. Any idea how to use color zone from the command line? thanks Giulia

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fit in map output : coordinate representation of axis, axis point
by Hwang, Youngha,Ph.D. 27 Jan '09

27 Jan '09

Hi, could anyone explain to me what axis points mean in chimera? What unit is used for them? Is it related to the volume dimension? Is the rotation matrix based on Euler-angle representation? Thanks, Youngha. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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3D on Chimera.
by ayassin＠wadsworth.org 27 Jan '09

27 Jan '09

Hello, I am trying to use Chimera to model pdb files into EM maps. When I select the red cyan stereo, the EM map is stereo but the pdb structure is not. -Is there anyway to display pdb in stereo in Chimera, how? -Is there another program that would allow me to do the same thing: fit pdb in EM density map-in stereo(other than "O")? -When I use Chimera on windows VISTA the side view panel does not appear and a message about graphic card appear, anyway to solve this? Thank you all very much. Aymen Yassin. Postdoc Research Affiliate Wadsworth Center, Albany,NY. IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

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marker coordinates
by Gabor Papai 27 Jan '09

27 Jan '09

Hi, I would like to do the following: I placed markers on density spots. I want to get their coordinates and excise a box around the marked density and save it as a separate file. For this I would like to know how I can retrieve the coordinates of a marker set and possibly how to position exactly a box around a marker to set a subregion (and of course how to set the dimensions of that box). This second feature existed before, but disappeared in the latest releases with the subregion selection tool in the Volume Viewer. Thanks in advance, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

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Volume information
by vamsee 27 Jan '09

27 Jan '09

Hello All, I am working on a virus and I am trying to figure out its volume. I would want to find out the volume of the nucleic acid and the water inside the virus capsid. That way, if I am thinking right, that should give me the total internal volume of the virus. This volume would be a constant even with the movement of water in and out. Is it possible to use chimera to calculate any of such data, with no prior information about how the nucleic acid is packed inside? Thanks in advance, Vamsee Graduate Student Dept of Chemistry and Biochemistry Montana State University Bozeman, MT - 59715

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suggested feature/model panel
by Matthew Dougherty 26 Jan '09

26 Jan '09

1) ability to create folders in the model panel so models can be grouped 2) ability to have a model in multiple folders 3) ability to show/hide in a folder by a a single checkbox 4) ability to name the folder

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How to display automatically the atoms in Gaussian cube file format
by Hyung Jun Lee 26 Jan '09

26 Jan '09

Gaussian cube file formats include the information about each atom's positions as well as the volumetric data. But, Chimera only displays the volumetric data when importing the cube file format. I want to know how to display automatically the atoms whose positions is included in the cube file, together with the volumetric data.

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Mac 64-bit Chimera version
by Thomas Goddard 26 Jan '09

26 Jan '09

Hi Denis, Conrad Huang in our lab tried building a 64-bit Mac Chimera several months ago. Many of the third-party packages we rely on failed to compile. We decided to pursue this only after Mac OS 10.6 is released. I believe the rationale of that was that Mac OS 10.5 is the oldest Mac OS that supports 64-bit graphical apps. We still support Mac OS 10.4 and our current automated build system targets 10.4. When 10.6 comes out we may target our builds to 10.5. Currently we only provide 64-bit Chimera on Linux. Tom Denis Chrétien wrote: > Dear Thomas, > > We were discussing some time ago about a 64 bit Mac version of Chimera. > Did you progress in this project ? (I'm still very limited for > visualization of large volumes with my mac, although its not a hardware > problem : 16 Gb Ram installed). > > Best regards, > > Denis > > Le 15 mai 08 à 18:41, Thomas Goddard a écrit : > >> Hi Denis, >> >> The Chimera error you reported means there was insufficient memory to >> compute the Fourier transform you wanted. I see from the report that >> your Mac has 18 Gbytes (wow). But our Mac Chimera version is a 32-bit >> program so its memory address space is only 4 Gbytes. In that 4 >> Gbytes has to fit not only data, but all shared libraries, program >> stack and (I think) operating system code. So really you might have >> just 3 Gbytes to work with. Also my Fourier transform code does a >> full complex value FT where it could do a real value FT taking half >> the memory. And the Python library that actually does the FT can only >> use double precision, so 16 bytes per complex value. More memory is >> used when Chimera takes just the magnitude of the FT coefficients. In >> short it is using 20 bytes per grid point. So a 512^3 FT will use 2.5 >> Gb, about the maximum that will fit in the 32-bit address space >> (assuming it isn't already fragmented by other data/libraries since >> you need a 2.5 Gb free block). >> >> We plan on fixing this. We plan on distributing a 64-bit Mac >> Chimera, and have tried compiling it. But some of the ~30 third-party >> libraries Chimera depends on did not compile. So we still need to >> work on that -- maybe within 3 months. Also I plan on making the FT >> code not such a hog, do a real FT and investigate 32-bit float FT >> values for a factor of 4 memory savings. For now your only option >> would be to use one of our 64-bit Chimera versions on Linux or Tru64 >> operating systems. >> >> Tom > > ___________________________ > Université de Rennes 1 > UMR 6026, équipe TIPs > Campus de Beaulieu, Bât. 13 > 35042 Rennes Cedex > France > > Tel. +33 (0)2 23 23 67 64 > http://www.umr6026.univ-rennes1.fr/ > ___________________________ >

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