- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [Chimera] #8137: undesirable window placement (was: Chimera bug report submission)
by Eric Pettersen 01 Feb '10

01 Feb '10

Guy Nimrod wrote: > When I do an action that opens a new window (e.g. ‘file’ -> ‘save > session as’ or ‘file’-> ‘fetch by ID’), it seems that the new window > is located in a random position. Sometimes it is out of the borders > of the screen which is very problematic. Hi Guy, I think the new window-placement behavior is an improvement for most people. Nonetheless, it seems to be a problem for you so I've changed it into a preference (with the new behavior as the default). Starting with tomorrow's daily build there will be a preference in the General category called "Try to avoid placing dialogs over main window" which you can change to "false". Unfortunately the daily build for Windows hasn't been working lately, so it may be a few days before you can get a version with this preference available... --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] holle,sir!
by Elaine Meng 30 Jan '10

30 Jan '10

On Jan 29, 2010, at 10:14 PM, gytjyb wrote: > holle,sir! nice to send a letter to you! > (1) about FindHBond .I can find out some HBond between ligand and > receptor,by chimera. I also use Accelrys Discovery Studio to find > out some HBond . but Accelrys Discovery Studio find out HBond to be > more than chimera. why?which one result is ture? > (2)what is meaning about Clashes/Contacts?what is useful for Finding > Clashes/Contacts > (3)how can i find out interaction between ligand and receptor and > classify displaying. > (4)can i use this software to publicate my paper ,directly? > best wishes for you ! (1) FindHBond vs. other programs. Different programs use different methods and cutoffs, and there is no reason to expect exactly the same results. The world of science does not agree on one exact definition of H-bond. Each program should explain its own method, as we have in the FindHBond documentation. Click "Help" on the FindHBond dialog or go here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon… > Also, this same question was discussed 2 days ago on the chimera-users list, see: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004746.html > (2) What are clashes and contacts? This is explained in the Find Clashes/Contacts documentation. Click "Help" on the Find Clashes/Contacts dialog or go here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas… > (3) use FindHBond and Find Clashes/Contacts. The "Structure Analysis and Comparison" tutorial is one example of using these tools: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> (4) yes, you can use images and calculation results from Chimera in your paper, but please remember to credit Chimera as described here: <http://www.cgl.ucsf.edu/chimera/docs/credits.html> Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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H Bonds in MD simulation
by snoze pa 29 Jan '10

29 Jan '10

Dear Chimera Users, I am analyzing a MD trajectory in chimera. After selecting H binds when I am playing the trajectory, then it always shows the hydrogen bond. Though some of the bonds are broken during the simulation but it always connect the step 1 h bonds connected.. How can I show the h bonds which breaks during the simulation. Thank you very much for your help. S

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Re: [Chimera-users] Rename atoms...and chains, residue numbers
by Jonathan Sheehan 28 Jan '10

28 Jan '10

On Mon, Jan 25, 2010 at 4:25 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > This is actually a little trickier than it really should be in the current > builds. As of tomorrow's daily build the following will work without any > issues to set the name of selected atoms to 'X1': > from chimera import runCommand > runCommand("setattr a name X1 sel") > --or-- > from chimera import selection > for a in selection.currentAtoms(): > a.name = "X1" Hi- Following up on this, I'd like to offer a feature request regarding structure editing. Two of the most common tasks I need to do when constructing a model are: renaming the chains in the structure, and renumbering stretches of residues. I can imagine two menu items similar to "Actions->Atoms/Bonds->Delete" named "Set chain ID..." and "Renumber residues from..." that could operate on the current selection. I suspect these menu options (or something similar, maybe under "structure editing"?) would be helpful to many folks. It could be a lot faster / easier than generating the right awk line or venturing into Emacs' PDB-mode. :-) Would this be difficult to implement? Thanks for considering it, -Jonathan -- Jonathan Sheehan, Ph.D. Comput. Biol. Educ. and Outreach Vanderbilt Univ. Ctr. for Struct. Biol. 5138 MRB3, 465 21st Avenue S. Nashville, TN 37232-8755

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Re: [Chimera-users] Chimera-users Digest, Vol 81, Issue 21 - chopped ccp4 maps in chimera
by Boaz Shaanan 28 Jan '10

28 Jan '10

Hi, The possible reason for the chopped ccp4 maps when they are displayed in Chimera (whereas they're fine Coot) may have to do with the fact that as far as I know Chimera does not apply the crystallographic symmetry operations to the ccp4 map (at least that's how it used to be in v1.3), whereas Coot does. So if the map is defined for the asymmetric unit only, it has to be expanded in order to cover all the region which one wants to display before being read into Chimera. There could of course be other reasons for the chopped maps. Cheers, Boaz ----- Original Message ----- From: chimera-users-request(a)cgl.ucsf.edu Date: Thursday, January 28, 2010 21:11 Subject: Chimera-users Digest, Vol 81, Issue 21 To: chimera-users(a)cgl.ucsf.edu > 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: Chimera movie question (Tom Goddard) > 2. Contouring ED Map: Sigma versus Chimera > thresholds (Veer Bhatt) > 3. Re: Contouring ED Map: Sigma versus Chimera thresholds > (Elaine Meng) > 4. Contouring ED Maps (Hector Viadiu) > 5. Re: Contouring ED Maps (Tom Goddard) > 6. H Bonds in MD simulation (snoze pa) > 7. Re: H Bonds in MD simulation (Elaine Meng) > > > ----------------------------------------------------------------- > ----- > > Message: 1 > Date: Wed, 27 Jan 2010 12:51:19 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > To: Bridget Carragher <bcarr(a)scripps.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Chimera movie question > Message-ID: <4B60A747.5030705(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Bridget, > > I put an example animation on the Chimera web site in the > animation > gallery called "Herpes virus slices". There is also a link > to a command > script which makes this movie. You just use File/Open... > in Chimera to > run the command script. > > > http://www.cgl.ucsf.edu/chimera/animations/animations.html > Tom > > > > > > OK, thanks Tom. Any tips on how to do all three planes > at once - or > > > rather keep the others constant while eating though the side > plane. I > > > have sen movies like this but can;t seem to figure out how > to do it in > > > Chimera. > > > Bridget > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 27 Jan 2010 19:12:31 -0500 > From: Veer Bhatt <veer82(a)gmail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Contouring ED Map: Sigma versus Chimera > thresholds > Message-ID: <C41C6E8E-343B-4FA1-BB71-49BAADB32DF2(a)gmail.com> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > Hi, > This in context of using Chimera to view *ccp4 format > electron > density maps. How does Chimera 'Threshold Level' ('Level' in > Volume > viewer) equate or relate to sigma level reported by some > other > programs. For example a 'Level' of 0.4 seems like a map > contoured at > 1.5 sigma or so. > I was wondering if someone could point out how these two are > related, > more precisely. > > Thanks > > Veer Sandeep Bhatt > >

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Contouring ED Map: Sigma versus Chimera thresholds
by Veer Bhatt 27 Jan '10

27 Jan '10

Hi, This in context of using Chimera to view *ccp4 format electron density maps. How does Chimera 'Threshold Level' ('Level' in Volume viewer) equate or relate to sigma level reported by some other programs. For example a 'Level' of 0.4 seems like a map contoured at 1.5 sigma or so. I was wondering if someone could point out how these two are related, more precisely. Thanks Veer Sandeep Bhatt

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lighting in Chimera
by Dan Gurnon 27 Jan '10

27 Jan '10

I wanted to tell you all that I love the new "glossy lighting" feature- now its easy to see the difference between the inside and outside of a surface when you use the per-model clipping tool. Without it, I had a hard time getting a sense of depth when a surface was clipped. But with the improvement glossy lighting brings, I have begun to wonder if other improvements in coloring and lighting are in the works or are possible. For instance, I use radial coloring with a grey palette to help my students pick out tunnels and pockets in a surface, but a better method would ambient occlusion on-the-fly. I've seen it in the molvis program "Qutemol", though the program does little else. Alternatively, is it possible to change the quality of shadows enabled in the effects window? And on a separate note, is it possible to change the inside color of a surface (something like "ribinsidecolor" for surfaces?) Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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running command scripts
by Michael Zimmermann 27 Jan '10

27 Jan '10

Dear Chimera users, I am getting to know Chimera a bit more and was just going through the scripting tutorial here: http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Scr… For the command line script 1gfl.com, the tutorial just says "run it" but does not say how. I just typed "run 1gfl.com" in the chimera command line, but I get a syntax error in the script. I can't seem to copy the error text, so a screenshot is attached. Is this an issue with the script or how I am running it? I use chimera v. 1.4 on win XP - 64bit. Thank you, Mike Z

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Rename atoms...
by Yasser Almeida Hernández 25 Jan '10

25 Jan '10

Hi.. How can i rename atoms? How would be the script python syntax? Thanks Best regards -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 246 ---------------------------------------------------------------- Correo FENHI

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Fitting a structure to a DAMMIN/SAXS model/volume
by Byrd, Robert A. (NIH/NCI) [E] 25 Jan '10

25 Jan '10

Chimera Team & users, We have been using SAXS data and the DAMMIN software from the Svergun group. The bead model that DAMMIN produces approximates the shape and volume of the molecule. If one has a three dimensional structure of the molecule, then it becomes valuable to do a best superposition of the structure into the bead-model shape. Chimera is our preferred molecular display & analysis software, and we would like to perform this fitting in Chimera. Do you have any experience in how to display the bead-model output of DAMMIN and to fit or superimpose the bead model with a known structure? Thanks Andy Byrd

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Re: [Chimera-users] Failed surface calculation
by Elaine Meng 25 Jan '10

25 Jan '10

Hi Ibrahim, First, make sure you set the New Surfaces preference value before showing the surface for the first time -- it would not affect a surface that already exists (even if it is hidden when you set the preference). If the surface already exists, you could change it to single-component by changing its attributes, such as with the command given in my previous message. However, if the Reply Log says there is only one component of the surface in both sets of parameters, I think it is still possible for a surface area to decrease when the VDW radii increase. I'm imagining a case where there is a lot of concavity. Similar to the situation of an inside bubble shrinking or disappearing, a concave part of the surface could become shallower or much less extensive as the VDW radii are increased. This is just a case I'm imagining. If you feel there is an error, please use "Help... Report a Bug" in the Chimera menu and be sure to describe exactly what you did to get the two area measurements, what two values you are comparing, and attach the PDB file of the structure (or just include the PDB ID in your description if it is taken directly from the Protein Databank). Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Failed surface calculation
by Ibrahim Moustafa 23 Jan '10

23 Jan '10

Dear Chimera, I¹m trying to calculate the surface for a protein but I get an error ²Surface calculation failed, mscalc returned code 5². I tried to change the probe size from 1.4 to 1.5 or 1.7 but still getting the same error. I know there is some issue with The code that calculates the surface (if I¹m not wrong) but I wonder if there is a way to get around this. For some smaller pdb files I don¹t have this problem. I¹m not sure if the size of the protein is a factor here. The protein having the problem is a single chain protein with 880 amino acids. Any advice? Thanks for help. Ibrahim

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Compatibility of Chimera with MacOS 10.4.11. PPC
by Arwid.Bierbach 22 Jan '10

22 Jan '10

Ldies and Gentlemen, The Chimera version Mac OS X (Aqua, PowerPC) chimera-alpha-osx_ppc_aqua.dmg Size: 73241868 bytes MD5: 39623fa9e0d9f4a869a4c985d45223bb Jan 22, 2010 is not compatible with G4 PPC Mac OS 10.4.11. Do you plan to quit the G4 PPC OS 10.4.11. - Compatibility ???? With best regards, Dr. Arwid Biebach, Germany

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Massive superposing...
by Yasser Almeida Hernández 22 Jan '10

22 Jan '10

Hi... I'm performing a massive superposing of aminoacids in different conformations. The first model is a arginine "template" reference structure that is the fixed model in all matching iterations. I've loaded 236 models and i want to match the arginine guanidine group on the template guanidine. In each iteration i execute two matching, with different atoms selections. The first selection is the "right" selection: CD,NE,CZ,NH1,NH2 and the second is the "inverse" selection: CD,NE,CZ,NH2,NH1. I run the two superpositions, and i want to show that with the minimal RMSD between the guanidine groups. This is the code: import chimera from chimera import runCommand right = "@CD,NE,CZ,NH1,NH2" inverse = "@CD,NE,CZ,NH2,NH1" for i in range(2,328): print "Superposing..." runCommand("match #"+str(i)+right+" #0"+right+"; close 1") right_rmsd = runCommand("rmsd #"+str(i)+right+" #0"+right+"; close 1") runCommand("match #"+str(i)+right+" #0"+right+"; close 1") inverse = runCommand("rmsd #"+str(i)+inverse+" #0"+right+"; close 1") if right < inverse: print "Minimum RMSD =",right,"\n\n" runCommand("match #"+str(i)+right+" #0"+right+"; close 1") elif right > inverse: print "Minimum RMSD =",inverse_rmsd,"\n\n" runCommand("match #"+str(i)+right+" #0"+right+"; close 1") In principle this script should show the matching with the minimum RMSD, but it doesn't work. Please, help... Thanks -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 246 ---------------------------------------------------------------- Correo FENHI

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Measuring Distances in Chimera
by Beale, John 21 Jan '10

21 Jan '10

Hello, I am trying to measure distances between atoms using the Tools -> Structure Analysis -> Distances routine. Chimera is requesting that two atoms must be selected in the main graphics window for this to work. I can't figure out how to select the atoms. Can someone help me? John

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Ligand Binding to Homodimeric Proteins
by Nancy 17 Jan '10

17 Jan '10

Hi All, I am performing molecular docking simulations of a ligand binding to a homodimeric protein, to determine a potential binding site(s). Due to the symmetrical nature of a homodimer, I would expect that the binding site(s) on one protomer would be identical on the other protomer. Therefore, a ligand should bind with equal probability and affinity to both sides of the protein. However, when I perform a molecular docking simulation (using an X-Ray crystal structure), the ligand preferentially binds to one side of the homodimer. Is this outcome likely the result of errors inherent in the X-Ray crystal structure, as one would expect identical binding to both sides? Thank you very much. Nancy

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adding hydrogens and charges
by Elaine Meng 17 Jan '10

17 Jan '10

> 1 how can i calculate the charges for molecular. > to calculate the charges both for ligand and receptor > individually. > if i want to do docking,if i must calculate charges. > 2 how can i add hydrogen for HIS. Maybe , no exact position for HIS. > how can i add hydrogen directly? > thank you very much! > Hello, Use the Dock Prep tool (in menu, Tools... Structure Editing... Dock Prep). It can do several things to prepare a structure, including adding hydrogens and charges. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ dockprep.html> Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] [chimera-dev] Calculating RMSD
by Elaine Meng 15 Jan '10

15 Jan '10

Hi Victor, I'll CC the chimera-users(a)cgl.ucsf.edu list -- that address is better for general Chimera "user" questions, while chimera-dev is more for "programmer" questions, i.e. involving python or other code. The "rmsd" command does not automatically use serial number to pair the atoms. You can control the order by specifying the residues and their atoms in the command. Of course, that can be painful if you want to include very many atoms in the calculation. If the order is not given in the command, "the atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number" as described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> You can see command manual pages using the "help" command, e.g.: help rmsd What approach is best depends on your particular case -- whether these are multi-residue macromolecules or single-residue small molecules, and how many atoms you want to include in the calculation. If they are single-residue small molecules, you might just modify the mol2 files so that the atoms you want to pair have the same names in the two structures (but unique within a structure). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 15, 2010, at 2:11 AM, Victor Muñoz wrote: > Hi, > I want to calculate the RMSD between two mol2 structures in place. > The two structures are different forms of the same structure. I > haver modified the mol2 so that the two of them have the same > serialNumber in their respective atoms. The problem is that when I > use the command rmsd #model1 #model2, it return an incorrect value > of the rmsd, as the value showed is too high, about 5, when it > should be about 1 (the two structures are very similar). Is there > any way to calculate the RMSD value in place correctly or I am > doing anything wrong? > Thanks for your help. >

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Re: [Chimera-users] [chimera-dev] adding an atom at the centroid of a blob
by Jean Didier Pie Marechal 14 Jan '10

14 Jan '10

Thanks a lot Elaine for answering me, I was indeed interested in both user interfase ...as well as the python shell one... best, jd Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Elaine Meng <meng(a)cgl.ucsf.edu> Data: Dimecres, Gener 13, 2010 11:26 pm Assumpte: Re: [chimera-dev] adding an atom at the centroid of a blob > > On Jan 13, 2010, at 8:01 AM, Jean Didier Pie Marechal wrote: > > > Hi everyone, > > I have obtained cavities for a given atom selection using surfnet > > > and I want to put an atom at the centroid of the main blob. I > know > > how to do this for a selected set of atom but I am struggling > with > > the surfaces. > > > > At this point, I splitted it (accelator Sc) and then I can select > > > the blob I am interested in. But how could I create a particular > > object for this blob? From there, how could I add an atom (i.e. > > helium) and the centroid of the blob? > > Thanks for any help, > > JD > > Hi JD, > > Now that you have your one surface piece selected (and nothing > else), > you could use the command "focus sel" or menu item "Actions.. > Focus" > to center the view on it, then add the atom at the center of view > with the Build Structure tool (under Tools... Structure Editing). > You would go to the "Add Atoms" tab in that tool, choose "atom" and > > click "Add." > > It may not be the centroid of the blob as calculated from its > vertices, but the center of its bounding box. You may want to try > it > and see if the result is sufficient. > > That's the user interface way. Maybe you meant in python -- if so, > > somebody else will have to answer! > > Best, > > Elaine >

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importing colored VRML file into cinema 4d
by odonnell＠chem.fsu.edu 14 Jan '10

14 Jan '10

Hello, I'm curious if anyone has had difficulty importing a colored VRML 3D object into Cinema 4D. I have exported a colored VRML file from chimera but the color is lost when opening it in the 3D graphics program Cinema 4d. Reopening the VRML file in chimera shows the color is there. Thanks in advance for your time. -Odie ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Re: [Chimera-users] [chimera-dev] adding an atom at the centroid of a blob
by Elaine Meng 13 Jan '10

13 Jan '10

On Jan 13, 2010, at 8:01 AM, Jean Didier Pie Marechal wrote: > Hi everyone, > I have obtained cavities for a given atom selection using surfnet > and I want to put an atom at the centroid of the main blob. I know > how to do this for a selected set of atom but I am struggling with > the surfaces. > > At this point, I splitted it (accelator Sc) and then I can select > the blob I am interested in. But how could I create a particular > object for this blob? From there, how could I add an atom (i.e. > helium) and the centroid of the blob? > Thanks for any help, > JD Hi JD, Now that you have your one surface piece selected (and nothing else), you could use the command "focus sel" or menu item "Actions.. Focus" to center the view on it, then add the atom at the center of view with the Build Structure tool (under Tools... Structure Editing). You would go to the "Add Atoms" tab in that tool, choose "atom" and click "Add." It may not be the centroid of the blob as calculated from its vertices, but the center of its bounding box. You may want to try it and see if the result is sufficient. That's the user interface way. Maybe you meant in python -- if so, somebody else will have to answer! Best, Elaine

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Looping with Chimera commands
by Yasser Almeida Hernández 12 Jan '10

12 Jan '10

Hi... It's possible run a Chimera's command iteratively? I have loaded several structures (more than 300) and i want to superimposed them to a reference structure. How i perform the matching command for every structure iteratively? Thanks -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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movie
by Alex Perálvarez Marín 12 Jan '10

12 Jan '10

Hi, I have the output files for an MD movie from Gromacs, an xtc and a tpr file. When trying to build the movie, Chimera ask for a tpr and trr files for the Gromacs input. I try anyway with my files but naturally Chimera crashes. Any help for this? Thank you in advance. Alex.

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problem to download chimera
by Gabriele Gucciardo 12 Jan '10

12 Jan '10

Dear Chimera developers, I have some problem to download Chimera. I'm trying to download the Chimera software. Once I clicked on the "download link" in the home web page of chimera, a new blank page was opened but nothing happened. I'm currently using Mac os X 10.4.11. I used browser safari 4.0.4 and Firefox 3.5.7, both gave same results. Kind regards, Gabriele Gucciardo School of Chemistry & Chemical Biology College of Life Sciences UCD, Belfield, Dublin 4 Ireland 00353 1 7162972 gabriele.gucciardo(a)ucd.ie

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showing conservation
by Elaine Meng 07 Jan '10

07 Jan '10

On Jan 7, 2010, at 6:30 PM, gytjyb wrote: > hello, > 1 how can i use this software to do molecular dynasty? > 2 can you tell me how to asure conservation sequence through > protein alignment. > maybe this is just for basic knowledge,but i am a freshman. > Hello, It is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of just to me. (1) maybe you mean molecular dynamics - sorry, Chimera does not do molecular dynamics. (2) I recommend going through some of the Chimera tutorials. There are some beginner tutorials and others that include showing conservation and aligning protein structures. You can see the tutorials by choosing "Help... Tutorials" from the Chimera menu, or by going to our web site: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html> Also, I have my own page on where you can get sequence alignments for viewing in Chimera: <http://www.cgl.ucsf.edu/home/meng/sources.html> Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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