- Chimera-users - RBVI Mailing Lists

How do I
by Eduardo Sanz Garcia 26 Nov '07

26 Nov '07

I am using Chimera alpha version 1 build 2467 2007/10/31 I liked how each volume map opened has a different color. That's a great idea!! But I have a problem, I am displaying 4 volume maps at the same time. The volume viewer window only shows 3 histograms, therefore to modify the threshold of the fourth I have to close one of the volumes. Is there a way to modify the fourth histogram in the volume viewer window without close another? I also found a different behavior if you close the upper, middle and bottom histogram. Thanks.

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saving color palette
by William Jeffrey Triffo 26 Nov '07

26 Nov '07

is there a way I can save the color palette to a file? I realize it seems to be saved as a user setting somewhere because it always pops up again in the same configuration as the previous session, but I would like to be able to back it up intentionally if possible. Also, is it possible to save/load various palettes? thanks, -Jeff --

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Chimera vs Amber, which one digresses from the average pdb rules?
by Francesco Pietra 26 Nov '07

26 Nov '07

A lipid/water pdb file that was good for Leap (Amber9) to get top/crd, once passed through Chimera 2470 to remove residues is no more good for Leap. All TER were removed by Chimera, ATOM renamed HETATM, while CONECT records were added. As such, Leap said: In file [chirality.c], line 142 Atom named C217 from POP did not match Aborting I knew such type of message. There is no C217 atom. On previous (different) occasions, insertion of TER records put the house in order. I inserted all TERs between POPC residues and between WAT residues (thanks to Python!). Now Leap said: In file [atom.c], line 444 bond AtomProblem found Aborting As I did not know this type of message, I tried to investigate that line 444. Following vim's command :n,444 that line, indicated at bottom of terminal as "444,1", reads HETATM 441 O31 POPC 5 -44.082 -12.831 14.685 1.00 0.00 O A carbon atom (if "[atom.c]" means carbon, is at line 447,1, which reads HETATM 444 C32 POPC 5 -46.343 -12.925 15.140 1.00 0.00 C In the original (good for Leap) pdb those lines read: ATOM 441 O31 POPC 4 -37.722 -19.453 18.019 1.00 0.00 L11 O ATOM 444 C32 POPC 4 -39.844 -19.273 18.941 1.00 0.00 L11 C Chimera also changed atom names, such as in the final part of the POPC residue (Sybyl naming?, if so, there is an alternative in Chimera not to follow Sybyl rules?) HETATM 528 XH14 POPC 5 -47.646 -9.424 -0.112 1.00 0.00 H HETATM 529 YH14 POPC 5 -46.217 -10.553 -0.172 1.00 0.00 H HETATM 530 5C31 POPC 5 -47.890 -11.168 -1.419 1.00 0.00 C HETATM 531 XH15 POPC 5 -47.763 -12.309 -1.296 1.00 0.00 H HETATM 532 YH15 POPC 5 -48.986 -11.063 -1.417 1.00 0.00 H HETATM 533 6C31 POPC 5 -47.242 -10.566 -2.756 1.00 0.00 C HETATM 534 XH16 POPC 5 -46.135 -10.759 -2.831 1.00 0.00 H HETATM 535 YH16 POPC 5 -47.802 -11.112 -3.597 1.00 0.00 H HETATM 536 ZH16 POPC 5 -47.451 -9.454 -2.737 1.00 0.00 H TER which, in the original (good) pdb was: ATOM 528 H14X POPC 4 -38.665 -14.879 4.398 1.00 0.00 L11 H ATOM 529 H14Y POPC 4 -39.080 -16.603 3.952 1.00 0.00 L11 H ATOM 530 C315 POPC 4 -40.370 -15.221 2.996 1.00 0.00 L11 C ATOM 531 H15X POPC 4 -41.330 -15.752 3.099 1.00 0.00 L11 H ATOM 532 H15Y POPC 4 -40.694 -14.148 3.019 1.00 0.00 L11 H ATOM 533 C316 POPC 4 -39.787 -15.573 1.664 1.00 0.00 L11 C ATOM 534 H16X POPC 4 -39.553 -16.661 1.544 1.00 0.00 L11 H ATOM 535 H16Y POPC 4 -40.534 -15.211 0.948 1.00 0.00 L11 H ATOM 536 H16Z POPC 4 -38.782 -15.094 1.533 1.00 0.00 L11 H TER Although it is not clear to me yet where really Leap crashed (nor am I placing Leap as the standard; simply I have to get top/crd from it, if I want to carry out MD with Amber). Elaine already kindly clarified the ATOM/HETATM issue. I hope now to get help about the atom names , ie a table of conversion to get Leap working or a not-Sybyl choice in Chimera. Once again, I regret very much to pose so many problems of language. Thanks francesco pietra ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

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<< Rendering proteins with Chimera >>
by Hatuey Hack 23 Nov '07

23 Nov '07

Hi all, As a Chimera new users, I notice that the proteins are rendering different depending on the program they where prepared. I used the preset to render them. I have a protein with all residues in different color and the other protein is rendered in a single color. My question is: this is a problem of Chimera or it is a problem with the protein file? Regards, Hatuey

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Aligning a protein into a membrane
by Francesco Pietra 22 Nov '07

22 Nov '07

Elaine: Relating to your instructions of last 19 Nov (I printed your mail, then unfortunately I deleted it) how to align a protein into a membrane (for both I have valid pdb and valid Amber parameters) I am probably made elusive mistakes at the stage of saving new pdbs. I aligned the protein into the membrane, then (with protein selected and membrane not active) I saved the new pdb, getting two files, "0" for the membrane and "1" for the protein. In Amber LEaP both these pdb file could be loaded and combined, however save top/crd failed because something was wrong with the membrane file. In fact, if the original pdb for the membrane is used, top/crd can be saved, though the protein is not accurately aligned. Clearly, my plan is to remove superimpositions among molecules for the "whole" obtained from Amber. 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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Re: [Chimera-users] ppt and movies
by Elaine Meng 22 Nov '07

22 Nov '07

Hi Markus, I can answer this one: > Why does the command movie record supersample 3 give virtually the > same file size then just movie record? Supersampling in Chimera initially saves a larger image for each frame but then samples it down to the requested size. This reduces "stairstepping" along edges without changing the pixel dimensions of the image that is ultimately saved for each frame. It increases calculation time rather than file size. Supersampling is also an option for saving individual images (File... Save Image) when you are not raytracing. You can see the difference provided by this feature independent of the movie-encoding process by comparing images saved with and without (1x1) supersampling. 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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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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Ribbackbone spec?
by Jean Didier Pie Marechal 14 Nov '07

14 Nov '07

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Z-slice transparency
by Lu 13 Nov '07

13 Nov '07

Dear Chimera Crew, Is there a way to adjust the transparency of a Z-slice using the Volume Viewer's "planes" feature? Right now, it looks like the Z-slice has transparency and lets you see the isosurfaces/segmentations below it. We would like to turn off the Z-slice transparency so that it blocks everything that is behind it. Such a feature would allow us to use Chimera to make a movie that we've been using Amira for, i.e., a movie in which the isosurface (or segmentation) is "revealed" as the map's Z-slice drops down. If the effect that I'm describing isn't clear, I'd be happy to forward a link to such a movie. Thanks! -Lu -- Lu Gan Postdoc, Jensen Lab Caltech Broad Center, MC 114-96 1200 E. California Blvd. Pasadena, CA 91125 Tel: 626-395-8848 Fax: 626-395-5730

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Computer requirements
by Sandra Eriksson 13 Nov '07

13 Nov '07

Hi! I'm planning to buy a computer, and am checking on the requirements of my favourite programs. But, searching the Chimera home page, I found little information on the hardware neccessary to make the program run really smoothly. If you have suggestions for RAM, processor and graphics etc, I would be very grateful. Best, /Sandra

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Question about the dotted bond
by Hyunmi Sun 13 Nov '07

13 Nov '07

Dear Whom it may concern Hello, I am currently using Chimera to access a pdb file. When I fetch the pdb file, one of the bonds between two ligands is illustrated as a dotted line in the wire representation. Why is this so? Thanks for the help! Sincerely, Hyunmi Sun

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Output of volume rotation angles and shifts in Chimera
by Duncan Sousa 13 Nov '07

13 Nov '07

Hi, I use Chimera to manually align 3D electron microscopy structures. I'm hoping someone knows how to output the angles and shifts of rotated and shifted volumes. Since one can restore sessions, the angles and shifts must be saved somewhere right? Thanks, Duncan __________________________________ Duncan Sousa, Ph. D. Department Physiology & Biophysics Boston University School of Medicine 715 Albany Street Boston, MA 02118

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Calculating the center of mass of a ligand
by Jean-Didier Maréchal 13 Nov '07

13 Nov '07

Hi everyone, I have another question: what would be the easiest way to calculate the center of mass of a given set of atoms? In particular, is there a python module that already has this function implemented? I am interested in particular to find the center of mass of a ligand bound to a protein. Thanks a lot, JD

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IDLE for listing selected residues.
by Jean-Didier Maréchal 13 Nov '07

13 Nov '07

Hi everyone, I'd like to use chimera to generate the list of the oxygen atoms of the water molecules located at less than 5.0 A of a ligand. Selecting the water molecules have been the easiest part... select :HOH & :301.a zr < 5.0 with :301.a my ligand. Then in the IDLE, I tried a series of alternative to generate the list. I use the different tips that were posted in the digest recently and arrived to this: for i in range(1,len(chimera.selection.currentResidues()): print chimera.selection.currentResidues()[i] Right, this gives me the list of residues, unfortunately, that would be a LOOOT better for me is to have the Serial number of the oxygen atoms... currentSerialNum and currentSerialNumber do not see to be a correct selection type. If there is any way that can do this? Thanks a lot JD On Sat, 2007-11-10 at 12:00 -0800, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Z-slice transparency (Tom Goddard) > 2. production release candidate (Eric Pettersen) > 3. pipes and planks (Dougherty, Matthew T.) > 4. Re: pipes and planks (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 09 Nov 2007 12:47:12 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Z-slice transparency > To: Lu <lugan(a)caltech.edu>, "'Chimera BB'" > <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4734C750.5020803(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Lu, > > I think I know why the volume planes are slightly transparent for > you. You are using Chimera version 1.2422 and I changed the volume > solid rendering transparency behavior in the later Chimera version > 1.2434 (August 3, 2007). You can either get the most recent Chimera > from the daily builds web page: > > http://www.cgl.ucsf.edu/chimera/alpha-downloads.html > > Or in older Chimera versions use volume menu entry Features / Brightness > and Transparency and change transparency to 0. You'll have to type this > in the entry field and press return because the slider does not go all > the way down to zero. This transparency value modulates the > transparencies given by the height of the brightness / transparency > yellow curve on the histogram. Newer Chimera changed the modulation > behavior to keep completely opaque voxels still completely opaque while > older Chimera did not. > > Tom > > > > ------------------------------ > > Message: 2 > Date: Fri, 9 Nov 2007 15:52:29 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: [Chimera-users] production release candidate > To: chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <7B31B33A-569C-4808-AD94-EBCD134DEC26(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi all, > We have put a production release candidate up for download (http:// > www.cgl.ucsf.edu/chimera/download.html) It would help us out if > people would try it out and see if it all works okay. Major changes > from the 1.2422 release include: incorporation of what were > previously "experimental features", such as morphing between volume > data sets; major revamp of the Volume Viewer interface; display of > dendrograms in Multalign Viewer; use of rotamer libraries in swapping > residue side chains and the ability evaluate possible swaps based on > clashing, fit into density maps, or hydrogen-bond formation. A more > exhaustive list of features is here: http://www.cgl.ucsf.edu/chimera/ > docs/relnotes/snapshot.html > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > >

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RMSD
by Julien Orts 13 Nov '07

13 Nov '07

Dear all, First thanks a lot for the great software you provide us!!! I would like to compare structures after an MD simulation. There is a function called match which can be used to calculate the RMSD between selected atoms. The protocol is the following; I select atoms within 5 Angstrom to a reference atom in the structure 1: 300 atoms selected. I do the same for the structure 2 (reference atom is the same): 311 atoms selected The problem is then I can not use the match function since the atom number is different. I selected then residues (the one which are 5A away from the reference atom) instead of atoms but it is a bit fastidious plus it is not the same as a "zone selection" (some atoms are coming even if they are at 5.6A) I print out (from a pdb) the number of desired proton but the command sel @123 do not work because atom selection is done by name and not by number (if it is really the case then it would be nice to have this possibility as well ;-) The last solution would be really easy and quick to do if the selection on atoms can also be done by number. Is there any way to solve this? I need to use all the atoms, so the matchMaker give me an RMSD but it does not use all of the atoms in the calculation of the RMSD. Basically I need the intersection of the two sets (two structures) of selected atoms. In reality I have much more than 2 structures so the protocol should also be scriptable, but I guess everything is scriptable in Chimera (right?) thank in advance many greetings Julien

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pipes and planks
by Dougherty, Matthew T. 09 Nov '07

09 Nov '07

I have about 80 pdb datasets, each corresponding to a single helix. I know I can do one at a time using the gui. What is the method for scripting? thanks, Matt Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

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