- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] chimera help - surface exposed sides
by Elaine Meng 22 Nov '07

22 Nov '07

On Nov 22, 2007, at 1:07 AM, Thomas C. Marlovits wrote: > Hi Elaine, > I am trying to find an easy way to determine solvent > accessible/surface exposed side chains but also buried side chains > from atomic structures. > The idea would be to: > - display the surface > - have a command that would highlight (color) surface exposed side > chains/amino acids > Optional: color the identified aa by physical property, etc > - show all the identified amino acids on a primary sequence > - write out the amino acids into a text file. > > Would be great if you can let me know, how to do this most efficiently. > Thanks, > -Thomas > ----------------------------------------------------------------------- > -------- > Thomas C. Marlovits, PhD, M.A.S. > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of > Sciences (IMBA) > Hi Thomas, - First assign atoms (or residues) an attribute with values equal to their solvent-accessible surface areas (more details below). - Then you can use Select... By Attribute Value to select any subset of those based on some cutoff, for example all atoms with surface area > 0. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#select The selection can be written as a list of atoms (or residues) with Actions... Write List, and the Sequence tool will show the current selection on the protein sequence (it would also be shown on a multiple sequence alignment associated with the structure, if you have such an alignment). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/seqpanel.html - Of course you could also color the selection, but now that numerical attributes are assigned, you can map values to colors that will gradually shade from one to another with "Render by Attribute" or the command "rangecolor" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html Now, back to how to get the attribute values assigned. Currently it is necessary to use the "Area/Volume from Web" tool (under Tools... Surface/Binding Analysis). It sends coordinates to the NIH StrucTools server. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html We are in the process of generating our own surface-calculation code that will provide these values within Chimera, but it is not done yet. The main inconvenience of this server approach is that you should first delete things like water and ligands if you don't want them lumped with the protein during the calculation. "Area/Volume from Web" has a few different options of what is calculated. You can use its MSMS method to calculate both molecular surface and solvent-accessible surface (this will generate two attributes) or the Gerstein method to calculate solvent-accessible surface. Atom attribute values will automatically be assigned by this tool. If you want them summed to residue attribute values, you must also use "Attribute Calculator". http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ calculator.html There are examples of using Area/Volume from Web, Attribute Calculator, and Render by Attribute in the Attributes tutorial, part 2: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ attributes.html#part2 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

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Coloring a surface according to distance from a selection
by Paul.Pillot＠ac-nice.fr 21 Nov '07

21 Nov '07

Hello, I can color a surface according to the distance from a single point or a plane, but is it possible to do it according to the distance from a selection (eg an other chain or molecule) ? My aim is to show the contacts between an antibody and an antigen. I tried the tool intersurf for doing it, but the result is pretty crude (low definition of the surface compared to the usual surfaces available). Thanks in advance, Paul

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spaceball 5000
by Jean-Paul Armache 20 Nov '07

20 Nov '07

hello, i have a question regarding usage of a 3d manipulation device. i have a spaceball 5000 device, which i would like to use under linux (or windows). is there a way of using this device in chimera? best regards, Jean-Paul Armache AG Beckmann LMU Gene Center

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move a structure into another one
by Francesco Pietra 18 Nov '07

18 Nov '07

I have installed chimera-1.2470 on Debian Linux i386. Thank you. I want to insert a protein into a lipid membrane in a precise opientation, then save the protein pdb in this configuration. I used VMD in the last few days to this redard. I wonder whether I can stick to Chimera for this purpose too. I tried by selecting "protein", though it was difficult to proceed. Thanks francesco pietra ____________________________________________________________________________________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/

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Puzzle with WAT
by Francesco Pietra 17 Nov '07

17 Nov '07

I am faced by a recurring puzzle with WAT (standard TIP3). In Amber9 xleap I loaded a pore protein_noH.pdb model getting top and crd files In both Chimera and VMD these showed that the WAT oxygen atom (natural, inside the pore) had been added of two hydrogens with intramolecular bonding between the two hydrogens. Otherwise, the geometry was correct for water. Correspondingly. in Chimera dockprep complained that one hydrogen of that WAT had incorrect valency, and refused to proceed. The protein.pdb created with ambpdb from such top and crd files showed the WAT correctly, without intramolecular H-H bonding. The geometry was exactly the same as for the above "wrong" WAT. With this protein.pdb, Chimera's dockprep was happy. That allowed docking with various (big) ligands, including amber re-score. I posted to dock-fans that the issue was solved, and how. Now I wanted to carry out Amber9 MD of that protein-ligand complex, inserting it into a lipid bilayer. I first tried the above protein.pdb alone into a membrane. A new venture for me. I posted separately a question how to create a hole around the protein. However, even when that is solved, I am faced again by the problem of viewing WAT into the pore as a triangle. Also, the many WAT mixed to the POPC of the membrane are also viewed as triangles. Actually, when that protein.pdb is loaded to xleap (as before leaprc.ff99SB and leaprc.gaff), the WAT into the pore is seen as a triangle. Thus, the protein.pdb, created with amdpdb is good for viewers and dockprep and docking, not back for LEaP. Although, it may seem as a loop, these are the facts (that so far I am unable to understand). I did not try yet if that allows MD, just because going on with such triangulated water seems unsafe. The protein.pdb ends as follows: TER ATOM 6885 O WAT 445 -0.036 0.094 -2.262 ATOM 6886 H1 WAT 445 0.921 0.094 -2.262 ATOM 6887 H2 WAT 445 -0.276 1.021 -2.262 TER END The membrane.pdb ends as follows: ATOM 50316 O WAT 3357 47.120 46.103 -26.069 1.00 0.00 W45 O ATOM 50317 H1 WAT 3357 46.727 45.819 -26.895 1.00 0.00 W45 H ATOM 50318 H2 WAT 3357 47.214 47.052 -26.153 1.00 0.00 W45 H END as a representative of the many WAT present. Thanks francesco pietra (the membrane was created with VMD and the file rearranged to be understood by Amber9) ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

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1.2470 production release available
by Eric Pettersen 16 Nov '07

16 Nov '07

Hi all, The production release, version 1.2470, is out now. A list of changes from the previous production release (1.2422) can be found here: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2470.html I think that page is pretty easy to scan through, but for those of us who are really time-challenged, the important changes, I think, are: 1) Incorporation of what were previously "experimental features", such as morphing between volume data sets 2) Volume Viewer improvements: a) Multi-data set interface b) Distinct initial map colors c) Resampling of rotated maps d) Improved large-file handling e) Single-plane display f) Scriptability 3) Display of dendrograms in Multalign Viewer 4) Use of rotamer libraries in swapping residue side chains with the ability to evaluate possible swaps based on clashing, fit into density maps, or hydrogen-bond formation Mac users with the new Leopard OS should note that it seems that 3- button mouse emulation is off by default in Leopard's X11. So, if you have a one-button mouse and want to be able to scale/translate using the mouse + alt/command, do the following: 1) click on the X11 icon (it should show up in the dock when you start Chimera) 2) open the X11 menu from the menubar at the top of the screen 3) choose the Preferences... entry 4) in the resulting dialog choose the Input tab 5) enable the Emulate three button mouse option --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Ramachandran Plots
by Quinton Dowling 16 Nov '07

16 Nov '07

Hi, I am interested in creating a ramachandran plot from an md trajectory. Particularly I would like to track the change in phi/psi angles over time for specific amino acids throughout the md in a fashion that is easily presentable. Is there a way to do this with Chimera? Or any way at all? Thanks a bunch. Quinton Dowling Research Computing Center The College of Idaho Caldwell ID 83605

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Re: [Chimera-users] Z-slice transparency
by Tom Goddard 15 Nov '07

15 Nov '07

I met Lu in San Diego and found out he was showing a volume slice and a second model which was also a volume using solid rendering style. The trouble is that Chimera cannot correctly display two transparent models -- at most one can be transparent. If two are transparent, the last one drawn (higher model id number) always appears on top of the other transparent models. This is a (serious) limitation of the Chimera graphics architecture. Technically Lu has the single plane set to be completely opaque, but all solid rendered volumes are rendered as if they have transparency even if the coloring is set for complete opacity. (The OpenGL z-buffer which records the depth of visible objects and prevents obscured surfaces from being shown is not used with "transparent" rendering). We tried using the TomoPlane Chimera extension from Karin Gross and Christoph Best and that draws truly opaque volume planes, but it is much slower. Tom Lu wrote: > Hi Tom, > > I tried everything that you mentioned, including adding multiple > points to the histogram, but I can still see stuff through the > Z-slice. Anyway, I noticed that you're going to be at the Scripps EM > workshop next week. If you have time at the workshop, I'd be happy to > show you the type of Amira movie that we'd ultimately like to make > using Chimera. > > Cheers, > -Lu

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mutation of residue
by hjoseph＠brandeis.edu 15 Nov '07

15 Nov '07

Hi everyone, I want to model my mutated residue into crystal structure and see its interactions. If anyone knows and easy way of doing it in Chimera please let me know. Thanks everyone, Helen Josephine

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how to make a bond
by dominique matt 15 Nov '07

15 Nov '07

I want to draw a bond between two atoms which appear linked by a dotted line. This is often the case when one atom is a metal. How can I draw the bond ? Thank you for your help Kind regards Dominique MATT Strasbourg

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