- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Chimera 1.8rc 64-bit as Default Application
by Antoine Maillard 28 Jun '13

28 Jun '13

Suggestion to Dylan Bennett / Chimera 1.8rc 64-bit as Default Application Hi Dylan, you asked how to get Windows 7 to acknowledge Chimera as the default program to open specific files. In my experience the same problem was solved by running Ccleaner up to 3 times in a row to fix registry keys. After the first run, re-scanning the registry with Ccleaner shows that .pdb entries still need to be fixed. I kept running Ccleaner on my computer's registry until it was deemed as clean and only then was file association successful. Hope this helps, Antoine

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Both chimera (x86) and chimera (x86-64) fail to run on Windows 8
by David Konerding 27 Jun '13

27 Jun '13

Hi, I have a Windows 8 pro machine, 64-bit 8 GB RAM Core i3 and Quadro FX 570. When I start Chimera (x86 and x86-64), I see the splash screen then it says "pythonw.exe has stopped working". When I add --debug: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics I managed to cause windows to try to send an error report, which captured these files: C:\Users\dek\AppData\Local\Temp\WERF405.tmp.appcompat.txt C:\Users\dek\AppData\Local\Temp\WERF464.tmp.mdmp if those are useful for debugging, I can provide them.

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Chimera 1.8rc 64-bit as Default Application
by Dylan J. Bennett 26 Jun '13

26 Jun '13

Hi, I am attempting to associate pdb and mol2 file types with Chimera 1.8rc in Windows 7. I have tried to set it using the right-click>open with... option in Windows as well as through the control panel. I select the chimera executable, but it does not seem to accept it as a valid program, and it returns to the previous screen without adding Chimera to the box for selection. I know this is not a Windows issue, as I can set other programs and it works fine. As well, I can set other programs for the mol2 and pdb file types. Is this a known issue, is there any work around. It's not the biggest deal, but it would make my life a little easier if I could do this. It used to work in the past, but just not with the latest version. Thank you and have a great day! -- -Dylan J. Bennett Dylan.John.Bennett(a)Gmail.com (914) 621-1149 Stony Brook University dylan.bennett(a)stonybrook.edu New York Medical College Biochemistry BSB Room 102 dylan_bennett(a)NYMC.edu

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Leap Motion
by Aurélien Grosdidier 24 Jun '13

24 Jun '13

Hi all, We're planning to try Chimera with the leap motion device (https://www.leapmotion.com/) Has anyone already succeeded to do so ? Best, Aurélien.

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modeling multimers
by Francesco Pietra 24 Jun '13

24 Jun '13

Hello: Modeling a trimer (all three chains present, though missing residues and atoms) with chimera and modeller installed locally. The default is modeling each chain, one at a time. The chains are identical in sequence but the X-ray structure shows different localized conformations. Question: is modeller modeling by taking the other two chains into account? If already answered, beg pardon. thanks francesco pietra

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Re: [Chimera-users] Chimera-users Digest, Vol 122, Issue 25
by Boaz Shaanan 23 Jun '13

23 Jun '13

Hi Francesco, I doubt that modeller knows how to take into account inter-subunit information. I would be surprised if it does. As far as I know, it's a sequence-homology based model building module which also uses fold recognition and probably other pieces of information but not about oligomeric arrangement. When I dealt with a similar problem (modelling a dimer) I modelled the subunit and then superimposed each of the two subunits on top of the corresponding subunit of the known dimer, followed by Chimera's matchmaker. The resulting dimer is still considered a hypothetical structure by me. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Sunday, June 23, 2013 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 122, Issue 25 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.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. modeling multimers (Francesco Pietra) 2. Fwd: modeling multimers (Francesco Pietra) ---------------------------------------------------------------------- Message: 1 Date: Sun, 23 Jun 2013 07:17:44 +0200 From: Francesco Pietra <chiendarret(a)gmail.com> To: chimera <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] modeling multimers Message-ID: <CAEv0nmt6Sy2MJcs=xk18qMGs2d5h0QOS_i7YXAJ1AEwpdWWsCQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello: Modeling a trimer (all three chains present, though missing residues and atoms) with chimera and modeller installed locally. The default is modeling each chain, one at a time. The chains are identical in sequence but the X-ray structure shows different localized conformations. Question: is modeller modeling by taking the other two chains into account? If already answered, beg pardon. thanks francesco pietra

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Re: [Chimera-users] Antw: Re: atomic models in pdf
by Tom Goddard 20 Jun '13

20 Jun '13

Hi Matthias, I think there are many ways to get Chimera output into 3D PDF if you are willing to drop $600 on commercial software. The trouble is that you have to produce the 3d model in U3D format and then the U3D can be embedded in PDF. Those two conversion steps, going from a Chimera 3d export format such as X3D to U3D and the U3D to PDF I believe can be done by many commercial applications. But I don't know free applications to do it. There may well be free applications but it might take a whole day of digging on the web to find them. If you do find them let us know. It is easier to find a commercial software conversion route. For instance PolyTrans ($395) from Okino Computer Graphics claims to read X3D and export U3D, and Adobe Acrobat Pro X ($200) can put U3D into PDF files. http://www.okino.com/conv/filefrmt_3dexport.htm http://help.adobe.com/en_US/acrobat/X/pro/using/WS58a04a822e3e50102bd615109… I've never tried this and would definitely worry about whether PolyTrans or any other software will faithfully handle Chimera's X3D output. I think the basic problem is U3D and 3D PDF are used by almost noone. The Okino web site gives some idea of the trouble with U3D: "Okino also has a long history involved with the U3D file format. U3D has quite a tainted history in the development community. It was derived from the old Intel IFX 3D gaming toolkit of the 1990's and forced upon developers as the Macromedia 'Shockwave-3D file format' in 2000. The Shockwave-3D format was abandoned in 2002 and then it resurfaced in 2004 when Intel forced it upon Adobe as the 3D file format to use within 3D PDF files (instead of Adobe using the better X3D file format). With the IFX toolkit being so buggy, Okino spent much of 2004 through to 2007 debugging the IFX toolkit and creating the main, defacto implementation of the U3D import/export converters." The AxPyMol plug-in you mention does not produce PDF (and is commercial, $148 academic, or $404 for a lab license, 1 year subscription). It embeds 3d PyMol scenes in PowerPoint -- there is no PDF involved as far as I can tell. It uses an Active X plug-in (only available on Windows). Tom On Jun 20, 2013, at 10:29 AM, Matthias Barone wrote: > Hi Tom and Conrad > Thank you for the fast replies and sorry for not being clear: > Im doing all presentations with the beamer package of latex and hence search an interactive way to show 3D models of x-ray protein structures instead of showing pictures. > What Im therefore searching is a way to make a pdf that provides me a 3D model (incl. mouse gestures like zoom, rotate, clip) with pre-set layout (ribbon, electron density colours and so on set in chimera). > > matthias > > > > > > >>> Conrad Huang <conrad(a)cgl.ucsf.edu> 20.06.13 19.16 Uhr >>> > Collada format is used by Apple's iBooks Author program to embed 3D > graphics. Collada files, with .dae extension, can also be displayed in > Apple's Preview application. > > I don't believe Collada is at all related to PDF, which uses U3D format > for 3D data. MeshLab is supposed to read many data formats, including > Collada, and generate U3D output. Unfortunately, Chimera Collada output > is not read properly by MeshLab; triangle per-vertex colors, specified > as an RGBA data source, seem to be ignored. Worse, saving U3D output > (so at least we get the geometric shape) also fails, producing, from > Chimera's 28MB Collada file, 2 1KB files (no, I don't think it's due to > compression :-) ). > > The bottom line is that I do not have anything new to contribute on the > PDF front. Sorry. > > Conrad > > On 6/19/2013 9:43 PM, Tom Goddard wrote: > > Hi Matthias, > > > > I'm not clear on what your goal is. You talk about embedding > > molecule models in PDF, in Latex and in HTML. > > > > Conrad Huang in our lab added Collada export to Chimera so that > > molecular models could be dropped into some ebook format but I'm not > > sure if that format was PDF or something else. Have to find out from > > him. We are also working on displaying 3d views of molecules in a web > > browser using WebGL and Chimera can export an html file for that. Those > > files tend to be large and you need a web browser that supports WebGL to > > view them. The Collada and HTML export are under Chimera menu entry > > File / Export…. The Collada export is in Chimera daily builds and HTML > > export is in Chimera 1.8. > > > > Tom > > > > > > On Jun 19, 2013, at 5:41 AM, "Matthias Barone" wrote: > > > >> Hi > >> I keep on searching for a solution for embedding atomic models in pdf > >> (by LaTex). In PowerPoint a plugin called AxPyMol does the job nicely, > >> but I want to use chimera. You were already discussing a similar topic > >> in > >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002663.html The > >> question in the topic was whether its possible to incorporate > >> mesh-data (via programs like MeshLab, Photoshop and the movie15 > >> package) into .tex files. > >> But Im searching for latex packages to display and manipulate atomc > >> models. Exporting in html could be a way to desplay everything but > >> electron densities (although html doesnt support mouse gestures) > >> sincerly, matthias > >> _______________________________________________ > >> Chimera-users mailing list > >> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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atomic models in pdf
by Matthias Barone 20 Jun '13

20 Jun '13

Hi I keep on searching for a solution for embedding atomic models in pdf (by LaTex). In PowerPoint a plugin called AxPyMol does the job nicely, but I want to use chimera. You were already discussing a similar topic in http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002663.html The question in the topic was whether its possible to incorporate mesh-data (via programs like MeshLab, Photoshop and the movie15 package) into .tex files. But Im searching for latex packages to display and manipulate atomc models. Exporting in html could be a way to desplay everything but electron densities (although html doesnt support mouse gestures) sincerly, matthias

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Ensemble cluster
by Damien Larivière 20 Jun '13

20 Jun '13

Dear All, As a preamble, it is quite possible that I completely misunderstood the way to use the Ensemble cluster tool. Here is the problem I face: I opened a PDB file containing 8 models. The models have the same number of atoms, the same numbering, the format is Model Endmdl, etc. I launched Ensemble cluster in order to identify clusters. From the image below, one can see visually 2 clusters. Chimera effectively identifies 2 clusters _but _the representatives of each (in red and blue-turquoise) belongs to the same cluster. I expected one representative in each of the two clusters. May you tell me what is wrong with my understanding? Many thanks for your help, Damien ps : Is there a way to cluster according to a previously chosen RMSD?

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Command line history
by Damien Larivière 20 Jun '13

20 Jun '13

Dear All, I just installed the last release for Windows (June 07, 2013). I would like to get back the command line history I had in the previous version. I saved this command line history in a file named/chimera.cmd/. May you tell where to copy/chimera.cmd/ in the program files of my new Chimera? (I've made a search in the Windows explorer for /chimera.cmd/ but nothing was returned) Thanks, Damien

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Hydrophobicity surface
by Anne Simonsen 19 Jun '13

19 Jun '13

Dear Chimera helpers, I'm trying to make a figure showing the hydrophobic surface of one chain (chain A in attached IGA1.pdb file) with a peptide (chain B) shown as ribbon with residues, but I then get a "hole" in the A surface around the peptide (see attached figure). Can you please advice? Thank you! Best wishes, Anne -- Anne Simonsen, PhD, Professor Dept. of Biochemistry, Institute of Basic Medical Sciences University of Oslo, P.B. 1112 Blindern 0317 Oslo, Norway Visiting address: Domus Medica, room 3174 Sognsvannsveien 9 0372 Oslo Phone: +47 22 851110 Fax: +47 22 851058 Mobile: +47 99350960 email: anne.simonsen(a)medisin.uio.no http://www.med.uio.no/imb/english/research/groups/autophagy/

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adding an O in compound 1
by Ibai Gazpio 18 Jun '13

18 Jun '13

Hi all, I'm trying to add an O molecule as compound 1 bound to a Fe of an Hem group. I use a program called GOLD to perform dockings but this doesn't recognize this O atom type, that is a O.3 type.. The output should be a mol2 file. Which atom type should I use? Ibai.

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Chimeras limited capability to visualize correctly molecular structure
by Marek Maly 18 Jun '13

18 Jun '13

Hello all, recently was sent to the Amber mailing list question about how to proceed here with simulation of the piece of graphene. I was just curious about the molecular structure so I tried to visualize attached PDB file in Chimera which was not able to show correct structure so I visualized it using VMD and also Vega ZZ in both cases without any problem. Then I used Vega ZZ to create MOL2 file and tried again to use Chimera for visualizing graphene saved now in MOL2 format but again without success. So maybe there is still some space for improvement of Chimera visualizing capability. Especially in case of MOL2 format I was surprised that Chimera is not able to show correct molecular structure as in this case all the information (including bonds/connectivity info) is included in the input file. All files are attached. (my version of Chimera is: candidate version 1.8 (build 38694)) Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Chimera - ball and stick - 3D printing
by Francois Richard 18 Jun '13

18 Jun '13

Hi everyone, I am trying to print a molecule from its PDB file (ID : 2BEG) using chimera and a 3D printer. I would like to print the ball and stick representation of the molecule, including the hydrogen bond. So far, (using this link : http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html) I played with molmap and volume commands and managed to print a volume but it does not include hydrogen bond. Do you have any idea how to improve the output? Thanks a lot, Francois

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protein schematic representaton
by francesco oteri 14 Jun '13

14 Jun '13

Good morning to everybody, someone of you knows whether exist a program that creates schematic representation of a protein like the one in plot b and d of the figure: http://www.nature.com/nature/journal/v427/n6972/fig_tab/nature02165_F3.html Greetings, Francesco

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Missing segment confuses addH
by Sam Egel 13 Jun '13

13 Jun '13

Hi, Basic Problem: I am attempting to use the addH tool on a metal containing active site I have extracted. The problem is that Chimera draws an 11 angstrom pseudo bond representing a missing segment between two residues. This bond seems to be the reason that a terminal carbon is receiving only two hydrogens rather than three. The pseudo bond runs right through the bond axis between two other carbons, both of which are protonated correctly. Can anyone please explain how to actually delete this bond (hiding through ~longbond, closing or hiding through the pseudo bond panel does not work) or provide another method to get this carbon to have three protons? I'm running v 1.6.2 of Chimera locally on Win 7 and the same problem occurs on a remote Red Hat Enterprise Linux machine running v 1.5 of Chimera. More Detail: Getting this carbon protonated in a one-stop-shop by Chimera would save me the world of time for a number of reasons, including that I need to make many files of this active site and every pdb of this enzyme has the same addH/pseudo bond problem between the same residues. The active site was extracted by writing a 10 angstrom zone around the metal to a pdb and then hand selecting the residues I cared about from there and writing them to a pdb. Workarounds: I have tried using command line ~longbond, hiding and closing out the missing segments option in the pseudo bonds panel, and deleting the bond by highlighting it and trying to delete bond under the adjust bond tab in modify structure window. If I write the pdb to an xyz (Molden) and open the xyz in Chimera, addH works just fine. However, I would really like for these files to be real pdbs that have associated residue names at the moment (residue names are, of course, deleted when converted to xyz). Thank you for your time, Sam

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display of glycine atoms
by Levandoski, Mark 11 Jun '13

11 Jun '13

Hello there - I recently got a new office machine and had to reload Chimera. Although I do not recall the number of the version I had used in the past, empirically I can tell that this is some updated version. My problem is that I am trying to display various residues of a protein selectively as space-filling ("sphere") on a ribbon frame. One residue of interest is a glycine. This version of Chimera seems incapable (or I am incapable of discovering how!) of displaying the various atoms belonging to this glycine residue. All other residues seem fine. Is this a glitch? Am I doing something wrong? For comparison, I have every confidence that this should work because with my older version of the program I was able to generate just such a view. Thank you very much in advance for the help, Mark P.S. By selecting the glycine of interest I am able to color the strip of ribbon by preset color, but not by element. Mark M. Levandoski Associate Professor of Chemistry Grinnell College 641-269-4544

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Selecting regions of a PDB structure
by Anindito Sen 11 Jun '13

11 Jun '13

Dear All, I have a pdb file of a large protein complex. I want to select several regions and color them differently to show the various domains. How can I do that. Thanks Andy Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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Re: [Chimera-users] movie of flying in a density map
by Tom Goddard 11 Jun '13

11 Jun '13

Hi Andy, The way to use saved positions in an animation is to save a session which includes all the saved positions. Then to make the animation you first open that session and then use the "fly" or "reset" command in a script with those named positions. This is a general method for making animations that works quite well. Setup everything in a session (which models are open, where they are placed, colors, lighting, background color, shadows, …), then just use an animation script to modify a few things. If you instead try to do all the setup in a script with no session it is much harder. I don't understand your question about clipping. Normally Chimera does not clip your maps when you zoom in. Only if you turn on clipping or make your view point move right through the map would you see clipping. Tom On Jun 11, 2013, at 1:07 AM, Anindito Sen wrote: > Hi Tom, > > In the Video tutorial about making a movie of flying through the protein complex - how can I have the positions saved (sav pos) and put it in a script. The idea is to modify a script that makes a density map rotate (which I already have) and then fly in through that. I can then alter the script accordingly to show different regions of the map (and will not need to type the whole set of commands). > > Secondly how can modify my script to zoom-in a density map without clipping the region of interest. It is obvious that a major portion of the map will be outside the view but the clipping plane will not move and clip the map (like when we zoom in manually in the Chimera window using the mouse. > > Thanks > > Andy > >> Dr. Anindito Sen (Ph.D) >> Department of Cell Biology & Anatomy >> Graduate School of Medicine >> University of Tokyo

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ligating two models
by Bala subramanian 06 Jun '13

06 Jun '13

Friends, What is the best method in chimera to ligate two models. I have generated a small ligand that has to be attached attached to a protein residue. Thanks in advance, Bala -- C. Balasubramanian

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Maximum volume size
by Tom Goddard 05 Jun '13

05 Jun '13

Hi Svetla, Chimera is correctly handling your 880x880x880 map. But by default Chimera displays only a single plane of very large maps, because the most common case of this is with tomograms where a single plane display is usually what you want. When it does this the Volume Viewer dialog shows a "Planes" slider in the dialog, and below that is a button "All" that will show all planes. If you want Chimera to always show the full map, use Volume Viewer menu entry Features / Data Display Options, and click off "Show plane when data larger than N Mvoxels", and then use Features / Save Default Dialog Settings so it will use that setting in all future uses of Chimera. Tom On Jun 5, 2013, at 9:54 AM, "Stoilova-McPhie, Svetla" wrote: > Dear Tom, > > Are there any limitation for the size of 3D map/volume the Volume viewer can visualize? > > We tried a 880x880x880 voxels map generated with spider and it comes out as a 2D map: 880x880x1. > WE triple checked and the volume file dimensions are indeed 880x880x880 and can be visualized as a 3D volume in the EMAN2 viewer. > > Please advise. > > Best regards, > > > Svetla Stoilova-McPhie, PhD > Assistant Professor, > Department of Neuroscience and Cell Biology > Scientist, Sealy Centre for Structural Biology > and Molecular Biophysics > University of Texas Medical Branch at Galveston > 301 University Boulevard, Galveston, Texas 77555-0620

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sementation
by Jingchuan Sun 05 Jun '13

05 Jun '13

Hello, After segmentation of a 3D map into 16 subunits and assign different colors, the saved .seg map does not save the color. During the preparation of our recent paper, we had to assign the color each time we open the .seg (hundreds of times), which make me very upset, even angry sometime. If the guy writing the program allow us to save the assigned color, that would have saved us many times. Thanks! Jim

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Re: [Chimera-users] Flip handedness of map
by Tom Goddard 05 Jun '13

05 Jun '13

Hi Michael, To flip the hand of map #0 use vop zflip #0 This makes a copy of the map with the z-planes in reverse order. Tom On Jun 4, 2013, at 9:09 PM, Michael Stowell wrote: > Tom, > > There used to be a simple way to change the handedness of a map in Chimera, just use a negative voxel number. However, this no longer works but rather gives an error. Is there a new way to achieve this. This is very helpful when assessing the handedness of EM maps. > > Thanks > > m > > Michael H. B. Stowell > MCD Biology and Mechanical Engineering Departments > University of Colorado > Boulder, CO

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Request for assistance
by Zachary W. Carpenter 04 Jun '13

04 Jun '13

Dear Chimera, I have been a long time user and really love your software. Recently I have used and cited Chimera in 4 high impact publications. One in mBio, two in nature medicine, and a final one in review at Nature Genetics. I have used Chimera to make beautiful images of mutations that we identify in NGS data of tumors. My role has become interpreting the effects of mutations on crystal structure. Thus far this has not been difficult as the effects of the mutations have been obvious. A recent finding however has left me extremely perplexed and I have need for greater accuracy of structural modeling of the mutations. I was wondering if you can put me in the right direction for creating models of mutations that are more reliable then just using Modeller or I-Tasser with the mutant in the sequence to be predicted. I know this is an elaborate question but I'd like to know which Chimera tools I can use to help me along this path. Or if I need to use totally new software/ methods. Thanks for your time, Zach -- Zachary W. Carpenter Department of Pharmacology College of Physicians and Surgeons Columbia University 630 West 168th Street New York, NY 10032 Email: ZWC2101(a)Columbia.edu

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To build ssDNA to base pair with the other strand of DNA
by Wei Shi 04 Jun '13

04 Jun '13

Hi all, I am working on solving the crystal structure of a protein-DNA complex. I could complete one strand of the DNA to fit the electron density using Coot, but for the other strand, the density for several bases at each end of the DNA is not clear and it's missing several bases at each end of the DNA. I am wondering whether in chimera, there is a function I could use to build the missing bases in one strand of the DNA to base pair with the other strand of DNA which is complete. Thank you so much! Best, Wei

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Re: [Chimera-users] Just starting out
by burt.goldberg＠gmail.com 03 Jun '13

03 Jun '13

Dear Elaine, it is very hard for Senior faculty to audit a class. As for the Biochemistry well I have been teaching it for several decades. My interest is to learn how to use Chimera better and I will be working with a post doc experienced in using Chimera. I just want to read so I can ask intelligent questions. I am employing this in an on going research project. Thank you again for you help. ------Original Message------ From: Elaine Meng To: burt.goldberg(a)gmail.com Cc: chimera-users(a)cgl.ucsf.edu List ReplyTo: chimera-users(a)cgl.ucsf.edu List Subject: Re: [Chimera-users] Just starting out Sent: Jun 1, 2013 12:53 PM Hi Burt, This forum is meant for questions about the Chimera program. Proteomics and informatics are vastly broader areas. You might want to look for recent textbooks and journal articles on those topics, and/or audit some classes, and/or attend the group meetings and seminars of academic researchers in those areas. It's not clear whether learning Chimera should be one of your goals at this point. Which tools and programs are needed depend on the research problem at hand, and the types of data that are available for tackling that problem. If you do want to learn how to use Chimera, there are indeed several step-by-step tutorials. Before doing any tutorials you can explore the website just to get a better sense of what the program is for: <http://www.cgl.ucsf.edu/chimera/index.html> The "Quick Links" section on that page includes tutorials. Best, 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 Jun 1, 2013, at 9:34 AM, burt.goldberg(a)gmail.com wrote: > Dear all, after 40+ years doing wet work I had to leave the bench, medical reasons, and so although my students continue doing work at the bench I have decide to go the route of proteimics and informatic for myself. The informatics is fine. How do I get started on the proteimics? Does the tutorial help? Any thing some one can suggest I read first? Thank, Burt > Sent via BlackBerry from T-Mobile Sent via BlackBerry from T-Mobile

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How to calculate the deviation of two ligands in the same pocket
by felipe vasquez 03 Jun '13

03 Jun '13

Hi, I am working on the modeling of one ligand in a native and mutant receptor. The ligand occupies different positions in the binding cavity, and I am interested in estimate this difference. However, if RMSD is calculated via MatchMaker, the ligand in mutant receptor (non-reference) is moved from its original position to try to minimize the deviation compared to ligand in native receptor (reference). How can I calculate the difference in the ligand position between the two receptors, in an appropriate manner? Best regards, * * *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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How to force Chimera to properly analyze and visualize in each MD movie frame the ribon representation of the protein structure ?
by Marek Maly 01 Jun '13

01 Jun '13

Dear all, I just found that if one loads several frames from the simulation (Amber prmtop + inpcrd, *.rst files) chimera calculate/set the character of ribons (random colil, beta sheet, alpha helix) just using the first loaded frame and even if structure of the protein is changing in the next frames (e.g. forming beta sheet structure from the originally random coil), the visual ribon representation is not changed. I found this, when I loaded just the isolated frame from the simulation and saw nice forming of the local beta sheet which was nicely highlighted by proper ribon representation (wide arrow) in the palce where was originally (in the initial frame) just random coil. But when I loaded both (initial frame and that after some MD simulation), chimera keep to use random coil representation for both frames. I did also reverse experiment i.e. first loaded later frame from MD simulation and then the initial frame and this time chimera fixed for both frames beta sheet representation in that protein area. Please is there any possibility to prevent such unwanted behavior and to force Chimera that analyses properly protein configuration at each loaded frame and eventually changes properly the ribon representation ? Thank you in advance for any useful advices ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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fetching EDS files from the web (python script)
by Laleh 31 May '13

31 May '13

Hello. I'm wondering how I can fetch a bunch of EDS files (from the EDS server) and save them in my local machine in .mrc format. I don't want to do this manually one by one from the user interface... I tried to use open_volume_file with different settings; but it is not working... I'm surprised because this is very starightforward with pdb files. I appreciate your help. Thanks in Advance, Laleh

3 2

castP, Chimera and atom numbers
by Boaz Shaanan 30 May '13

30 May '13

Hi, Apparently Chimera insists on consecutive serial atom numbers (the first column after ATOM in the pdb file) when it reads in castp files. If that's not the case (as most often happens when hydrogens are attached during the refinement run but are not written out to the final pdb) Chimera complains about incompatibility between the mouth file and coordinates and refuses to read in the castp files. This is my first encounter with a program that cares about the atom number column but I learnt it the hard way. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

2 1

Tube representation picture of the eigenvector
by Prasanna Venkatesh 29 May '13

29 May '13

Dear Chimera users and supporters, I would like to generate a tube representation picture similar to one in the article (Figure 5 in "MD Simulations of Papillomavirus DNA-E2 Protein Complexes Hints at a Protein Structural Code for DNA Deformation"). Through Gromacs, I have average.pdb and extreme.pdb of my protein for the MD simulations. Please help me by providing the steps to make the picture. I asked the question earlier but not getting the similar picture with the answer provided. I don't know I asked it right the last time. Thank you in advance. Regards, Prasanna.

3 4

How to deselect a subset of atoms in a non-standard residue
by felipe vasquez 28 May '13

28 May '13

Hi, I am trying to select all hydrogens atoms in a protein structure to achieve an energy minimization process. However, I would like to discard of the selection the hydrogen atoms of a non-standard residue (in my case a cofactor, NADPH). How can I deselect only this subset of hydrogen atoms of the whole hydrogens selection? Best regards, *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

2 2

How to delete range of solvent molecules
by felipe vasquez 22 May '13

22 May '13

Hi, I am trying to prepare a protein structure for docking, and I want to keep just one or a couple of water molecules. How can I do achieve this goal, deleting the rest of solvent molecules? Thanks in advance. Best regards, * * * * *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

2 1

Distance measuring
by T-I 22 May '13

22 May '13

Dear Chimera, I want to know something very simple which is making my life very difficult at the moment. I have an EM map of a virus capsid and I would like to make various distance measurements. I simply want to draw a strait line and measure it or place two points on the map and measure the distance between them. I have read all your help files on this matter and I cannot make any sense out of the instructions Can you help me out ? Thankyou Mr A.I

2 1

Fitmap in batch mode
by ingvar 22 May '13

22 May '13

Hello, I am trying to run fitmap on a set of volumes on a server without a display. I would like to collect the results of the top hits to store in a database – correlation coefficients, inclusion scores, and the transforms. The only way I found to collect the fitting results is to save the session after displaying the listFits dialog. The listFits dialog cannot be displayed when running Chimera in –nogui mode, otherwise this would have been a solution. I tried to use a virtual display, with Xvfb. I have used Xvfb with some java applications in the past. When I use Xvfb with Chimera, it appears that Chimera do not want to start up properly, the process just hangs, i.e. no cpu usage. Is there a way around this, or am I asking for an enhancement, e.g. a “writeListFile toFile” option. I am on RHEL 6.2/6.3 if that matter. Noticed that there is a local correlation option in the pipeline for Chimera 1.8, looking forward to try it out. Kind Regards, Ingvar Typical python script: from chimera import runCommand as rc rc("open emd_5500.map") rc("volume #0 level 1.34 transparency 0.5") rc("open emd_2017.map") rc("volume #1 level 0.58 transparency 0.5") rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2 listFits false") #rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2") rc("save session5500_2017") rc("stop now") Setup to run with Xvfb (in bash): i=0 while [ -f /tmp/.X$i-lock ] do i=$[$i+1] done Xvfb :$i & pid=$! export DISPLAY=:$i chimera fit5500_2017.py kill $pid

2 2

Pipes and planks representation
by Ernesto Arias Palomo 21 May '13

21 May '13

Dear chimera developers, I have noticed that in the last Chimera releases you have significantly improved the 'pipes and planks' representation. I find it particularly useful because, in my opinion, it makes the structures look simpler and clearer, especially when you are displaying large PDBs. I would like to suggest an improvement. It would be really useful if you could make that representation an attribute of the structure (like the 'ribbons' one) instead of a separate object. That way one could easily show, hide or color different regions of the structure without having to modify the actual PDB file. Thank you very much for your help, and congratulations for your great work. Cheers, Ernesto.

2 1

Re: [Chimera-users] RMSD i.b and RMSD u.b
by Elaine Meng 20 May '13

20 May '13

Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of just my address. The RMSD lb (lower bound) and RMSD ub (upper bound) of a docked ligand are calculated by AutoDock Vina and are described in the manual for that program: <http://vina.scripps.edu/manual.html> (go to that page and search for "RMSD") I believe they just indicate how similar each position is to the best-scoring position found. 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 May 20, 2013, at 6:10 AM, Muhammad ALi <muh.ali741(a)yahoo.com> wrote: > AOA > > sir > when I check my result with ViewDock their are two RMSD values i.e RMSD i.b and RMSD u.b plz tell me about them.....

1 0

3D Printing our protein
by Bart Janssen 20 May '13

20 May '13

Hi My apologies for what are likely to be stupid questions. We are plant developmental biologists and we just obtained our first X-ray crystal structure for a new hormone receptor in plants. We'd really like to make a 3D model of the protein using one of the 3D printers at our institute. I've been trying to use and understand Chimera for the last week and I'm a bit out of my depth :). I can import our protein 4DNP.pdb and display it using solid surface or using the sphere representations of atoms. I can also display it with the "lid" domain hidden and vice versa. My problem has been getting files that our 3D printer can read. The solid surface model of the whole protein can be exported as a scene in .stl format and that can be printed just fine. Although I can't figure out how to adjust resolution or the smoothness of the exported file. But I'd really like to print the two domains of the protein separately. If I use Solid surface model with the lid hidden what I get is an eggshell like model which has no internal detail. If I use atoms shown as spheres instead I get the internal detail I want BUT when I try and export the scene I get a 2 Gb+ file that is unreadable by the printer. If I export .obj format instead the colleague who runs the printer says the file won't load and appears to have errors. I have a horrible feeling I am going about this entirely the wrong way but I can't find a tutorial that describes what I'm trying to achieve. I do realise chimera is not really written for the somewhat trivial use that I am attempting but it really would be helpful if we had a physical model of the protein to look at. Is there a tutorial I should follow or another part of Chimera (or another program) that I should be using instead? Any advice would be much appreciated. Cheers Bart Bart Janssen Scientist Plant Development team Breeding and genomics Plant and Food Research Private Bag 92169 Auckland 1142 New Zealand Ph +64 09 9257179 bart.janssen(a)plantandfood.co.nz The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited.

5 7

showing salt bridges in pdb trajectory movie
by Albert Lyons 18 May '13

18 May '13

Hi all, I am having a problem trying to show salt bridges between selected atoms in a movie of my pdb format trajectory. I am using the following commands in the Per-Frame script, to display H-bonds between the residues but with a less strong distance criterion (to bring the distance of interaction to 6 A) and angle criterion (to make the angle 0deg and so make all angles available): select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 When I apply this script I get a Chimera error saying: Error while sourcing select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 ,line 1: "findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145" Non-alphanumeric character in keyword ':6@2HH2,2HH1,HE,2HH1,1HH1' I have tried tweaking it different ways but just get other error messages, I can't seem to write it in the correct format. Can anyone see a problem with this script and how I might fix it? Cheers Albie

2 1

showing salt bridges in pdb trajectory movie
by Albert Lyons 18 May '13

18 May '13

Hi all, I am having a problem trying to show salt bridges between selected atoms in a movie of my pdb format trajectory. I am using the following commands in the Per-Frame script, to display H-bonds between the residues but with a less strong distance criterion (to bring the distance of interaction to 6 A) and angle criterion (to make the angle 0deg and so make all angles available): select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 When I apply this script I get a Chimera error saying: Error while sourcing select :1,6,7,10,16,18 findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145 ,line 1: "findhbond selRestrict :1@HZ1,HZ2,HZ3 :6@2HH2,2HH1,HE,2HH1,1HH1 :7@O3P,O2P,O1P :10@HZ1,HZ2,HZ3 :16@HZ1,HZ2,HZ3 :18@2HH2,2HH1,HE,2HH1,1HH1 linewidth 2 reveal true relax true distSlop 2.97 angleSlop 145" Non-alphanumeric character in keyword ':6@2HH2,2HH1,HE,2HH1,1HH1' I have tried tweaking it different ways but just get other error messages, I can't seem to write it in the correct format. Can anyone see a problem with this script and how I might fix it? Cheers Albie

1 1

Re: [Chimera-users] Conserved amino acids
by Rebecca Swett 17 May '13

17 May '13

Use match-> align to get a structural superposition and sequence alignment, then set your alignment type to AL2CO. Go to render by attribute and then hit the select by attribute tab. Select the range from 0-whatever your maximum is. Should be around 4 if you've got any conserved tryptophans. That will select all invariant residues. Jean-Paul Boissel <boissel(a)uni-mainz.de> wrote: >Hi, > >By homology modelling, I got putative structures for five closely related >amino acid transporters. Is there any script that will allow the quick >selection and visualisation of the invariant residues on the structures? >Thanks, > >Jean-Paul > > > > > >_______________________________________________ >Chimera-users mailing list >Chimera-users(a)cgl.ucsf.edu >http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

2 1

Conserved amino acids
by Jean-Paul Boissel 17 May '13

17 May '13

Hi, By homology modelling, I got putative structures for five closely related amino acid transporters. Is there any script that will allow the quick selection and visualisation of the invariant residues on the structures? Thanks, Jean-Paul

1 0

Carbon color of 1 chain
by Markus Heller 16 May '13

16 May '13

Hello, I don't seem to be able to figure out how to color a scene by element, but with different carbon colors for different chains. I can't figure out how to get an expression like "color green, chain C C" Or something like that ... How to go about this? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:kessabar@cdrd.ca> | www.cdrd.ca

4 7

Re: [Chimera-users] energy optimization of the modle from homology modeling
by Elaine Meng 16 May '13

16 May '13

Hello, I agree with what Tom Goddard said: "How to make a suitable homology model for docking and what force fields to use are not questions specific to Chimera, they are questions about how to do good quality science, and they depend a great deal on the details of your system. So you aren't likely to get the answers you want on this list." Instead, you have to use your scientific judgement and your knowledge of this protein, how similar it is to the template protein, etc. The procheck statistics are only one thing to consider. One reason is that they are for the whole protein, whereas you mostly care about the binding site. Another is that they focus on stereochemical quality, mainly torsion angles, but not other descriptors such as whether the protein is well packed. You could see what others have done in published papers, and/or ask on the Computational Chemistry List (see <http://ccl.net/cgi-bin/ccl/send_ccl_message>) and the Modeller discussion forum (see <http://salilab.org/modeller/discussion_forum.html>) if it is recommended to minimize homology-modeled structures before docking. In complicated structures like proteins, atoms may "feel" multiple conflicting forces, and minimization will usually relieve some strains (for example, move atoms apart if they are too close together) but increase others (for example, distort the angles of the sidechains containing those atoms). That is why the statistics from procheck got worse. It is important to realize that minimization has very little ability to fix a complicated structure with a rugged energy landscape. It is good for cleaning up small molecules, and sometimes for cleaning up a localized area (leaving the rest of the protein unchanged) where you have made some change such as manually rotating some bonds or mutating a residue. It will not predict any significant conformational change to find the global optimum. If you don't have any specific reason to minimize the structure, it might be better not to minimize it. That is only my guess, and you could probably get more expert opinions by asking your question on the other discussion lists mentioned above. If your docking doesn't take too long, you could try docking to more than conformation of the protein (more than one model). Chimera does not do molecular dynamics, although it can show MD results from other programs. However, Modeller itself does sampling to generate multiple models. Also, you could consider using Modeller to further refine parts of the model(s) from the first Modeller calculation. The Modeller scores should provide some indication of which models and refinements are better. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> 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 May 14, 2013, at 9:39 AM, Conrad Huang wrote: > Unfortunately, that is getting well beyond my understanding of molecular mechanics. I will have to defer this to our expert when she returns. > > Conrad > > On 5/13/2013 7:56 PM, aixintiankong wrote: >> Dear, >> Thank you for your patience to answer my questions in detail. >> Before /minimizating/ the model, i use the procheck to check the >> quality of the model. the residues in most favoured regions is 95.6% and >> the disallowed regions is 0.0%, the the residues had an averaged 3D-1D >> score>0.2 is 92.02% and the errat is 90.55. >> if i use the chimera to minimizate the model after 200 steps, the >> most favoured regions is 85.5% and the disallowed regions is 0.4%, the >> the residues had an averaged 3D-1D score>0.2 is 99.2% and the errat is >> 95.968. >> if i use the chimera to minimizate the model after 250 using the >> ff99sb! force filed, the most favoured regions is 92.1% and the >> disallowed regions is 0.4%, the the residues had an averaged 3D-1D >> score>0.2 is 96.96% and the errat is 98.000. >> if i use the chimera to minimizate the model after 500ns the most >> favoured regions is 90.8% and the disallowed regions is 0.4%, the the >> residues had an averaged 3D-1D score>0.2 is 96.58% and the errat is 96.047. >> which one model should i select to make docking . >> thank you very much! >> >> At 2013-05-14 00:24:03,"Conrad Huang" <conrad(a)cgl.ucsf.edu> wrote: >>> Unfortunately, our local expert on this is on vacation and will be back >>> at the end of the week, so a more definitive answer should come then. >>> In the mean time, I'll try to answer as best as I can. >>> >>> First, Homology Modeling uses Modeller and that does a bit of >>> optimization already. If the model structure looks reasonable, further >>> energy optimization might be helpful. On the other hand, if the model >>> has extended chains because Modeller does not have appropriate templates >>> or just looks unreasonable because the model is not well packed or has >>> large dangling loops, then energy minimization probably will not help. >>> >>> Second, I do not know the answer, but have you tried using the default >>> paramters? >>> >>> Third, conjugate gradient is much much slower than steepest descent, so >>> it probably pays to use steepest descent to get near the minimum before >>> starting conjugate gradient. You can look at the reported energy values >>> reported to decide whether the minimization is proceeding as expected. >>> Chimera energy minimization is not highly optimized, so it may take a >>> while to run for a large system. If only one portion of the model is >>> "interesting", e.g., an active site, it might be faster to select just >>> the region of interest (plus a buffer around it) and only optimize that >>> part. >>> >>> Hope this helps a bit. Better answers should come later in the week. >>> >>> Conrad >>> >>> On 5/11/2013 6:50 PM, aixintiankong wrote: >>>> Dear, >>>> i am a newer use the chimea, i have some question to consult to you, >>>> please help me. >>>> Frist, after Homology modeling using the chimera modeller, should i >>>> optimizate the modle by energy optimization or Molecular dynamic >>>> simulations? The next step i will use the model to make docking. >>>> Second, i want to use chimera to minimize the structrue of my modle. >>>> i select Tools>Structure Editing>Minimize Structure to perform my >>>> work, but my modle include protein and a organic molecule NAD+, so i >>>> don't know how to select the force fileds for the minimiztion of the >>>> modle. please help me. >>>> Third, if i olny want to use the conjugate gradient to perform the >>>> minimiztion, should i only need to set the steepest descent steps to 0? >>>> in general, how many conjugate gradient s! teps and size should be ? >>>> Thank you very much!

1 0

Error reading PubChem3D SDF Files
by Jon Fuller 15 May '13

15 May '13

I tried to read an SDF file directly downloaded from pubchem into Chimera. However, I ran into the following problem (link to example file used, and reply log below). Is this expected behaviour, or a bug? Additionally I tried to import the pubchem CID 71739 (same compound) from the fetch structure by ID tab, and got the error message: Unexpected end of file (parser state: counts) in MOL/SDF file 'FILEPATH HERE!' Many thanks in advance, Jon http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=2385389770715… You are now running Chimera version 1.8 (build 38642). Your previous version was 1.5 (build 32133). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) Error while processing CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_3672_e5800000001_conf.sdf: Non-numeric charge (1 -0.65) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data

3 4

energy optimization of the modle from homology modeling
by aixintiankong 15 May '13

15 May '13

Dear, i am a newer use the chimea, i have some question to consult to you, please help me. Frist, after Homology modeling using the chimera modeller, should i optimizate the modle by energy optimization or Molecular dynamic simulations? The next step i will use the model to make docking. Second, i want to use chimera to minimize the structrue of my modle. i select Tools>Structure Editing>Minimize Structure to perform my work, but my modle include protein and a organic molecule NAD+, so i don't know how to select the force fileds for the minimiztion of the modle. please help me. Third, if i olny want to use the conjugate gradient to perform the minimiztion, should i only need to set the steepest descent steps to 0? in general, how many conjugate gradient steps and size should be ? Thank you very much!

3 2

desmond in chimera
by lecan 15 May '13

15 May '13

Hi to everybody. Can the newest version of Chimera use the .cms files from desmond by schrodinger to analyse trajectories and make movies? Regrads, Luis L.

3 2

surface
by Gesa Volkers 14 May '13

14 May '13

Hi chimera users/developers, I have a problem with a surface calculation from one monomer of a structure that I want to show. As you can see in this image http://imageshack.us/photo/my-images/801/testss.png/ it looks like the surface calculation failed (?) because the surface is missing in the middle (note the chewed up structure of the surface). Most of the surface is smooth but for whatever reason not this part of the structure. I have played around with probeRadius, vertex density and zone and they all increase quality but do not add the missing surface part (I'm not even sure if zone is applicable to surfaces at all or only to electron density maps). Any suggestions which parameter I am missing? Thanks for suggestions, Gesa

2 2

Contour maps or step-gradient of volume map?
by Bullitt Esther 13 May '13

13 May '13

Hi, Is it possible to choose n levels of gray for a volume map? I'd like to make a known-thickness slice using clip, and then see that slice as a defined number of colors. I can kluge it by displaying the map 4 times at 4 contour levels, but is there a better way? thanks, Esther --- Esther Bullitt, Ph.D. Dept. of Physiology & Biophysics Boston University School of Medicine 700 Albany Street, Room W302 Boston, MA 02118-2526 Email: bullitt(a)bu.edu Telephone: 617-638-5037 Facsimile: 617-638-4041 http://www.bumc.bu.edu/phys-biophys/faculty/bullitt

2 1

mask using volume contour surface
by gongpu zhao 13 May '13

13 May '13

Hi All, I have a question about volume contour surface in chimera. I have a density volume of a shell shape. I plan to use the outer contour surface of the volume to mask out all density encased by the outer surface in a tomogram. But instead, I could only mask out the density within the shell. I am wondering if I can make a surface model only using the outer surface. Thanks a lot. Gongpu

2 1