- Chimera-users - RBVI Mailing Lists

Fwd: accessible surface area for electron density maps
by David Chenoweth 27 Mar '09

27 Mar '09

Begin forwarded message: > From: David Chenoweth <dchen(a)caltech.edu> > Date: March 27, 2009 8:58:31 AM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] accessible surface area for electron > density maps > > Hi Elaine and Murali, > > I have a similar problem that I've been trying to resolve. > Calculating the accessible surface or solvent accessible surface is > also something I've been interested in doing with Chimera but I > don't think the area of the molecular surface is the same as the > solvent accessible surface area. I believe that accessible surface > comes from the locus of the center of a spherical probe as it rolls > over the Van der Waals surface of a molecule. The molecular surface > uses the locus of the inward facing spherical probe. They both > depend on the spherical probe size which is set to the appropriate > solvent molecule. Can you tell me which of these two methods Chimera > is using when it calculates the area (if either)? Is there a way to > calculate the solvent accessible surface area of a molecule with > Chimera or some way to manipulate the current area calculator to > give this value? I also think that depending on the quality of the > electron density map one could get very different results for this > calculation (especially if there is missing electron density or at > different map contour values). If anyone has any advice for the best > way to calculate solvent accessible surface area I would really > appreciate the help. > > Thanks, > Dave Chenoweth > > ********************************************** > David M. Chenoweth > California Institute of Technology > Division of Chemistry and Chemical Engineering > Mail Code: 164-30 > 1200 California Boulevard, 91125 Pasadena > California, USA > > Phone: 626-395-6074 > Email: dchen(a)caltech.edu > ********************************************** > > On Mar 27, 2009, at 8:14 AM, Elaine Meng wrote: > >> Hi Murali, >> If I understand correctly, you want to get the area of a contour >> surface of the density shown using the Volume Viewer tool. If you >> want the total surface area, even of multiple separate blobs, use >> "Measure Volume and Area." If you want to measure the area of >> different blobs individually, use "Measure and Color Blobs." >> >> These can be started from the Tools menu of the Volume Viewer dialog, >> and also from the main Chimera Tools menu (Tools... Volume Data... >> [name of tool]). >> >> For more details on how to use a tool, press the Help button on the >> dialog. That opens the documentation included with your download. >> Our web site also has copies of the documentation: >> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/measurevol… >>> >> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/pickblobs/… >>> >> >> 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 Mar 27, 2009, at 7:42 AM, Murali Ayaluru wrote: >> >>> Dear Chimera users, >>> I want to calculate the accessible surface area for an electron >>> density map (mrc format) that I am working on. Can anyone, who >>> knows how to do this, tell me how to do this? >>> Thanks in advance for your reply, >>> Regards, >>> Murali >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > >

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Re: [Chimera-users] accessible surface area for electron density maps
by Elaine Meng 27 Mar '09

27 Mar '09

Hi David, As soon as you show a molecular surface, both the total solvent- excluded (molecular surface by Richards definition) and solvent- accessible areas are reported in the Reply Log. It has been like that since before the July 2008 release. The surface that is actually displayed is the solvent-excluded surface. You can adjust parameters that affect the results such as probe radius and atomic radii, but the defaults are reasonable. The area values are also assigned as per-atom and per-residue attributes named areaSES and areaSAS, so you can use Attribute Calculator to get sums over subparts of the surface. For details, see this page and links therein: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ representation.html#surfaces> I hope this helps, 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 Mar 27, 2009, at 8:58 AM, David Chenoweth wrote: > Hi Elaine and Murali, > > I have a similar problem that I've been trying to resolve. > Calculating the accessible surface or solvent accessible surface is > also something I've been interested in doing with Chimera but I > don't think the area of the molecular surface is the same as the > solvent accessible surface area. I believe that accessible surface > comes from the locus of the center of a spherical probe as it rolls > over the Van der Waals surface of a molecule. The molecular surface > uses the locus of the inward facing spherical probe. They both > depend on the spherical probe size which is set to the appropriate > solvent molecule. Can you tell me which of these two methods > Chimera is using when it calculates the area (if either)? Is there > a way to calculate the solvent accessible surface area of a > molecule with Chimera or some way to manipulate the current area > calculator to give this value? I also think that depending on the > quality of the electron density map one could get very different > results for this calculation (especially if there is missing > electron density or at different map contour values). If anyone has > any advice for the best way to calculate solvent accessible surface > area I would really appreciate the help. > > Thanks, > Dave Chenoweth

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Re: [Chimera-users] accessible surface area for electron density maps
by Elaine Meng 27 Mar '09

27 Mar '09

Hi Murali, As far as I know, there is no definition of accessible surface area for an electron density map (and thus no way to calculate it in Chimera), only for atomic structures. I'll describe how to get it for atomic structures in my next message, replying to David. Best, 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 Mar 27, 2009, at 8:18 AM, Murali Ayaluru wrote: > Hi Elaine, > > Thanks for the quick reply. I am aware of calculating the total > surface area of the density maps using Chimera and has been using > it for a long time. Now I am interested in the surface area that a > solvent can access (in otherwords called - (solvent) accessible > surface area). This is a part of the total surface area. Please > mail me if this tool is available in Chimera. > > Regards, > Murali

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accessible surface area for electron density maps
by Murali Ayaluru 27 Mar '09

27 Mar '09

Dear Chimera users, I want to calculate the accessible surface area for an electron density map (mrc format) that I am working on. Can anyone, who knows how to do this, tell me how to do this? Thanks in advance for your reply, Regards, Murali

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Bonds vs. Pseudobonds
by Dipl.-Ing. Thomas Mitterfellner 24 Mar '09

24 Mar '09

Hello again! I have a structure containing Germanium bonded to three oxygens and one methyl group. By default, all of the bonds between Germanium and its valences are considered as pseudobonds and hence drawn as such. In the manual, I read that Chimera uses an algorithm that considers atoms classically bonded if the distance is below the sum of their VDW radii (plus a margin of 0.4 A). However, no matter what I set the radius of the Ge atom to (setattr a radius xy Ge), I can't get Chimera to display a regular bond between Ge and its valences. Can you give me a hint how to set a rule when a normal bond is drawn, or how I can draw one manually? Thank you very much, Thomas

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Using per-frame scripts with color by attribute/bfactor
by Andrew M. Simms 24 Mar '09

24 Mar '09

I am making some MD movies using the multiple-pdb file format. I am using coloring by attribute, in this case overriding the "bfactor" attribute for my own purposes. The nature of my analysis is such that the bfactor can change from frame to frame. I use this command in the per-frame script: rangecolor bfactor,a min white max green However, when I try to make a movie, it appears that the bfactor attribute changes are not reflected in the animation. If I look at generated structures individually they are fine. Is there something special I need to specify in per-frame script? Thanks! --Andrew

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Split colors from Volume Viewer
by Damien Larivière 23 Mar '09

23 Mar '09

Dear Chimera team and users, When opening a map (EMD 1126 for example), the structure is displayed in grey. From the menu Volume and Surface colors, it is then possible to color the structure. I would like to export in the OBJ format the colored structure but this one still appears in grey when I display it in a modeler such as 3DSMax. And effectively, the MTL file created by the exporter only contains one color although the structure displayed in Chimera was multicolored. I look at a tutorial explaining that it is possible to Split map from the menu Volume/color zone. It seemed to me that it is a way to get a multicolored structure in the OBJ format. However, when I want to "split map", a message says "no atom selected". May you tell me how to get a multicolored structure (initially opened from a map) in the .obj format ? All the best Damien

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amd64 installation
by Francesco Pietra 23 Mar '09

23 Mar '09

To deal with very large data files i tried to install chimera-1.3.2577-linux_x86_64.exe in /usr/local/chimera. Mainboard Tyan S2895 dual-opterons; OS Debian amd64 lenny; nvidia chipset 6600, nvidia-glx driver To simplify i made the chimera directory to belong to me as user. The installation from my home succeeded, though chimera did not launch. It appears in part for a moment as if there were no opengl support: francesco@tya64:/usr/local/chimera/bin$ ./chimera X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 3 (X_GetWindowAttributes) Resource id in failed request: 0xffffffff Serial number of failed request: 626 Current serial number in output stream: 627 I installed libmotif3. Same issue. Once the problem of running chimera is solved, I plan a reinstall in /usr/local/chimera root root. Should I run the installation from my home as superuser? thanks francesco pietra (I run successfully the 32 bit version of chimera on an old Athlon with libmotif3 support)

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addna?
by julien(GWDG) 23 Mar '09

23 Mar '09

Dear all, I would like to know if there is a way in chimera to add nucleic acid to an existing RNA. Something like addna instead of addaa. many thanks Julien -- European Molecular Biology Laboratory Structural and Computational Biology Unit Meyerhofstraße 1 D-69117 Heidelberg Max-Planck-Institute for Biophysical Chemistry NMR based Structural Biology Am Fassberg 11 D-37077 Göttingen

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Re: [Chimera-users] UCSF Chimera
by Elaine Meng 22 Mar '09

22 Mar '09

On Mar 22, 2009, at 8:36 AM, Tarit Mitra wrote: > Dear Dr. Meng, > I am trying to learn to use the Windows version of Chimera. I would > like to contact a Chimera user in UK. Is it possible to do so? Can > you please help? > With kind regards > Yours sincerely > Tarit Dear Tarit, You could try the e-mail list chimera-users(a)cgl.ucsf.edu (actually I cc'ed it on this message). However, you don't need a live person to help you learn how to use the program. The Chimera download includes several tutorials, some for beginners: choose "Help... Tutorials" from the Chimera menu to see the list. Our Web site has additional tutorials (not just the ones in the Help menu): <http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html> Besides the tutorials, there is a complete user's manual (choose Help... User's Guide from the Chimera menu). Just start Chimera and try one of the beginner tutorials, or just experiment, and you will gradually learn! Best, Elaine

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Changing properties by command line
by Dipl.-Ing. Thomas Mitterfellner 19 Mar '09

19 Mar '09

Hello again! I could not find out how to change radii of selected atom via the command line. I had hoped this would work via '@/radius=', which I read in the quick reference, but I turns out that I obviously misunderstood the usage of the hints given there. Is it also possible to change the color and linestyle of coordinative bonds in the command line? Related to this: can the status and color of the molecule silhouette be changed from the command line? Thank you very much! P.S.: Chimera really produces great pictures and I especially like the silhouette effect, which I, up to now, always had to (partially) draw myself with some image editor.

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Chimera does not always recognise atom name in PDB ATOM records
by Christian Schudoma 19 Mar '09

19 Mar '09

Hello Chimera-Users and -Devs, I encountered the following problem when trying to visualise the following purine molecule (Actually, I tried to do something more complex(*) but the same problem can be reproduced with this more simple example). For clarification, the first lines contain the column numbers. 1 2 3 4 5 6 7 123456789012345678901234567890123456789012345678901234567890123456789012345678 HETATM 1 N1 CKN A 1 -0.003 1.586 -3.371 0.00 0.00 N HETATM 2 C2 CKN A 1 1.016 1.511 -4.278 0.00 0.00 C HETATM 3 N3 CKN A 1 2.313 1.566 -3.865 0.00 0.00 N HETATM 4 C4 CKN A 1 2.576 1.683 -2.541 0.00 0.00 C HETATM 5 C5 CKN A 1 1.559 1.758 -1.597 0.00 0.00 C HETATM 6 C6 CKN A 1 0.224 1.717 -2.032 0.00 0.00 C HETATM 7 N7 CKN A 1 2.100 1.858 -0.373 0.00 0.00 N HETATM 8 C8 CKN A 1 3.434 1.842 -0.568 0.00 0.00 C HETATM 9 N9 CKN A 1 3.731 1.742 -1.876 0.00 0.00 N When I load a pdb file containing these coordinates into Chimera, I get 9 non-connected dots (obviously representing the atoms) which can neither be coloured by hetero-atom, nor by element. Note that the atom names are located in the appropriate columns, i.e. between columns 13 and 16, more specifically in columns 15 and 16. I noticed that in other pdb structures 2-character atom names are located in columns 14 and 15 and when I put my atom names there, Chimera displays the purine ring system which then can be coloured by hetero-atom/element. Now it is nice that this workaround fixes my problem, however, according to the pdb file format specification (columns 13-16 are reserved for the atom name), atom names located in columns 15 and 16 are valid(*) and as such should be processible by visualisation tools etc. The behaviour occurs with the latest daily build as well as some older versions I found on my hard disk... (*) The purine is part of a larger cytokinin. I stumbled upon the described behaviour while using the AddHydrogen function on the whole molecule, which lead to the replacement of the purine with a hydrogen. (**) Unless there are some additional rules regarding the placement of atom names shorter than 4 characters, in which case I apologise for bugging you with this. Any comments on this? Best regards, Christian Schudoma -- Christian Schudoma, M.Sc. Bioinformatics Group System Integration Group Max Planck Institute of Molecular Plant Physiology Am Muehlenberg 1 14476 Potsdam-Golm Germany phone: +49 331 567-8624 email: schudoma(a)mpimp-golm.mpg.de http://rloom.mpimp-golm.mpg.de

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Re: [Chimera-users] Making movies
by Elaine Meng 19 Mar '09

19 Mar '09

> Hi Elaine, > BD simulations is brownian dynamics. Well my file is in a PDB > format, and basically consist of a single complex, with heteroatoms > living from one active site to the other. If you open the file as a > pdb file you will realized the heteroatoms HOH are static. But I > want them to be able to move from the active site of one enzyme to > the other in the complex. > > I was thinking that I can put the word Model, between the complex, > and each heteroatom HOH, so as to make the file seem to have many > pdb files. Hi Neville, Yeah, I eventually realized you meant Brownian dynamics! But what matters for Chimera is the format rather than how the trajectory was generated. To use "MD Movie" to play/record the trajectory, your PDB format options are: (a) put each frame in a separate PDB file The file names must include frame numbers, and files for all intermediate frames must also be present. The files must not contain END records. (b) put all the frames in one PDB file, but bracket each with MODEL and ENDMDL, as is done for NMR ensembles in the Protein Databank, e.g. 1g1p. The MODEL numbers are interpreted as frame numbers and should start with 1 or 0 and increment by 1. Either way, atom names, residue names/numbers need to be the same between frames. ** In general, each frame should have the same number of atoms. However, for "weird" cases where lots of atoms stay in the same position (which if I understand correctly is what you have), we have made a special provision: if the coordinates supplied for a frame represent only a subset of the atoms in the preceding frame, it will be inferred that the remaining atoms are present but have the same coordinates as in the preceding frame. Changes are cumulated in the forward direction and based on all frames, even when frames are skipped during playback. All of the atoms must be in the first frame, of course. In your case, I guess that would include the proteins plus the starting locations of the heteroatoms. You might need to renumber the HOHs to keep their identities across the frames... looks like what you sent gives each position a different residue number. This information as well as how to play the trajectory and record it as a movie are in the MD Movie manual page (choose Help... User's Guide, click Tools tab, click link "MD Movie"). I hope this helps, 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

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Question about adding a sequence to a previous structural alignment...
by Sergio Garay 18 Mar '09

18 Mar '09

Hi all I've prepared an structural alignment of my 3 protein templates using MatchMaker/Match-Align tools. The question is: when I add my target sequence to the profile obtained in the step before, Does this procedure change my previous structural alignment?, or It just aligns the added sequence to my profile. The parameters that I used to add my target sequence are: Blosum-62, gap open, and gap extension penalties: 12 and 1 respectively. The second problem I have, its not related to chimera, but may be one of you can answer it. My target only has 29 % of identical residues with my templates, so Should I use a less stringent parameters to make my alignment? Any help would be appreciated. -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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save image error in current daily build
by Ryan Pavlovicz 18 Mar '09

18 Mar '09

Hello, when trying to save an image with the current daily build of Chimera, i am finding that the program closes with the following error: X Error of failed request: BadAccess (attempt to access private resource denied) Major opcode of failed request: 129 (GLX) Minor opcode of failed request: 10 (X_GLXCopyContext) Serial number of failed request: 0 Current serial number in output stream: 15993 Just wanted to let you know. Thanks, ryan

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Re: [Chimera-users] merge mrc volumes
by Anindito Sen 18 Mar '09

18 Mar '09

Hi Tom Carsten actually just took away my question. Thanks Carsten! It will be really helpful to have such feature ! Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 --- On Wed, 18/3/09, Tom Goddard <goddard(a)cgl.ucsf.edu> wrote: From: Tom Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] merge mrc volumes To: carsten.mim(a)yale.edu Cc: chimera-users(a)cgl.ucsf.edu Date: Wednesday, 18 March, 2009, 5:43 AM Hi Carsten, There's no facility in Chimera to combine (add) maps into a single map though it has been requested by many people and I am anxious to add such a command. Tom carsten.mim(a)yale.edu wrote: > Hi there, > I constructed a model with different .mrc files. Now I want to save the model as > a merged *.mrc file, containing all previous files. > > Thanks > > Carsten > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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merge mrc volumes
by carsten.mim＠yale.edu 18 Mar '09

18 Mar '09

Hi there, I constructed a model with different .mrc files. Now I want to save the model as a merged *.mrc file, containing all previous files. Thanks Carsten

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Changing default element colors
by Dipl.-Ing. Thomas Mitterfellner 17 Mar '09

17 Mar '09

Hello! Can the default element colors be changed easily and if so, how? Thank you, Tom

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Chimera
by taritkumar MITRA 17 Mar '09

17 Mar '09

Dear Sir, I have just installed windows version of Chimera. I am a retired Chemist taken up Molecular Modeling as a hobby. I have some experience of using Spartan and Hyperchem. I would very much like to use the Chimera specially for studies Docking. Are theire any publication or books which will help me in learning to use Chimera. I f so I would like to buy it. Can you please help? With regards Tarit taritmitra(a)hotmail.com

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DICOM maps
by triffo＠rice.edu 17 Mar '09

17 Mar '09

anyone out there know the easiest way to get a DICOM map (typical format for medical CT/MRI data; volume density map; .dcm file extension) into chimera? Is there a translator out there that will reformat DICOM data into a chimera-friendly volume map? thanks, -Jeff

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heme (fe) containing enzyme
by Agus Setiawan 17 Mar '09

17 Mar '09

Hi, I'm a student of Pharmacy and I just learn about chimera.Actually, I want to run a docking using Autodock so I have to minimze the structure of macromolecule first. I choose Chimera to minimize the structure of macromolecule. However, there is an error because the Fe atom doesn't have GAFF"Unable to find GAFF type for #0:500.A@FE"I also have a problem with hydrogen at Histidin residu"no MMTK name for H at standard HIS"How can Isolve this problem?I'll be very thankful for your answers.Best Regards, Agus Lee.

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Re: [Chimera-users] Making movies
by Elaine Meng 17 Mar '09

17 Mar '09

On Mar 16, 2009, at 10:13 PM, yimnai forlemu wrote: > Hello Elaine, > I have a quick question and was wondering whether I can use chimera > to archieve my goals.I have ran a BD simulation and saved > trajectories of my particles. My question is whether it is possible > for me to use chimera to create a movie from the BD simulations > trajectory data.If yes please could you just direct me to the > tutorial that can help me accomplish that goal. > Thanks > Neville Hi Neville, I don't know what "BD simulation" is. Chimera's "MD Movie" tool can read trajectory output from several programs: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h… > If you have one of those formats, or can convert your output to one of those formats (for example, multiple PDB files), MD Movie can show the trajectory. You can control how the molecules look in Chimera as you normally do, then use "File... Record movie" from the MD Movie dialog to create a movie. This tutorial uses the MD Movie tool to do various things, including saving a movie: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#p… > There are other ways to save a movie (not necessarily using the MD Movie tool). This page has more general information including links to example scripts and other movie-making tutorials: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html> I hope this helps, Elaine P.S. For a reliable response, please send mail to chimera-users(a)cgl.ucsf.edu rather than to me directly. If you send mail to only me and I'm run over by a bus, you will never get an answer!

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Session management suggestions
by Thomas Goddard 16 Mar '09

16 Mar '09

Matt Dougherty sent 4 session file management suggestions. 1) Session description text, browsable. 2) Copying camera positions between sessions. 3) Session version numbers with matching filename extensions. 4) Automated checkpoint session saving. Details below. Tom Matthew Dougherty wrote: > 1) I frequently have to use a lot of session files in combination with a > lot of command files to generate animations. > > One session file might be used with multiple command files. > > I try to pack as much information into the filename as a way to keep it > all organized, but this is becoming cumbersome. > the filenames are becoming cryptic to keep them short; plus I multiple > drafts I need to maintain in case the researcher wants to go back to a > prior visualization. > > It would be good to have a item in the' File' pull-down-menu to handle > summaries or descriptions. > > By activating it, I could type in a paragraph as to what is going on > with the session. > > In a bigger picture, it would be good to be able to start chimera, and > somehow peruse through these descriptions, but not have to load the > session to read the description. > > 2) many times in an animation project I start with a common session file > containing all the data sets in sync, and create multiple derivative > session files to handle different aspects of the animation, usually with > the unused datasets deleted for a particular animation session for > reasons of improving computation speed and loading for a particular > animation clip. > > sometimes I would like to move a set of camera positions created in one > of the daughter session files to another daughter session file. > > Matthew Dougherty wrote: > 1) optional automated versioning. Sometimes I when I am working on an > animation I need to keep the intermediate versions, particularly when I > am less certain about what I am doing and the complexity of the session > goes up. > > check box somewhere that causes saving to automatically prepend "_V22" > before ".py", for version 22 in this example, and _V23 for the next > save, etc. > > 2) optional automated checkpoint saving such that the interval time can > be set. sometimes when working on a complex session it get a crash and > I have not saved it, so I have lost all my work from the previous save, > which could be 1-4 hours.

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Octamer to dimer
by John Lowenstein 16 Mar '09

16 Mar '09

Dear Folks, In PDB 1ewj the structure comes up as an octamer. The physiological entity, in which I am interested, is a dimer. I can eliminate three of the for dimers, but I have not found a way to eliminate the six extra ligands (bleomycin) associated with the three eliminated dimers. (I want the dimer with two ligands.) Any suggestions? Thanks. Sincerely, John Lowenstein

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confocal stack
by Benoit Zuber 16 Mar '09

16 Mar '09

Hello, Is it possible to browse through the planes of more than 1 volume at a time? I have some confocal data and I want to browse along the X axis of the dataset; each volume corresponds to a confocal channel. Cheers, Ben

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