December 2012 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! 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 Apr 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

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font size in pull-down menus
by Boaz Shaanan 09 Oct '13

09 Oct '13

Hi, Is there a way to change the font size of the pull-down menus? For some reason on the Windows (XP) v.1.5.1 they seem smaller to me. Nothing in terms of graphics (or my eyesight) has changed since I upgraded to 1.5.1 recently. Thanks, Boaz Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Circular DNA minimization
by Damien Larivière 03 Jan '13

03 Jan '13

Dear all, I'm currently minimizing a circular DNA molecule, relatively large (~11 000 atoms). I use "Minimizing structure" in Structure editing. The first phase, the Steepest Descent Steps, works fine. However, the second one, the Conjugate Gradient Steps, looks like blocked with the message "dock prep finished" at the bottom of the screen. If I remove one base pair so that the molecule is no more cyclized, then the second minimization stage starts as expected. I'm not versed in the art of minimization. Do you know the reason of this behavior? Thanks for your help, Damien ps: I'm working on Windows 7 with a core i5

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GLYCAM force fields and Chimera
by john Kerk 28 Dec '12

28 Dec '12

Dear Users I want to assign the partial charges of a glucose molecule using chimera-1.7 but I can not find this force field in Add charge suite although the GLYCAM force field files are existing under amber12. can I get help wishing merry Christmas , John

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a PyMol file into Chimera
by Anindito Sen 21 Dec '12

21 Dec '12

Dear All, Questions of the following type/s may have been answered many times before but will be of help if you can reply (again). I have a PyMol file with file extension 'pse' . I want to Visualize it Chimera. Is there any trick to do that ? Best 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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More on initial energy value from Chimera
by Thomas Sturgill 20 Dec '12

20 Dec '12

Elaine has explained that the initial energy is a total energy and not a free energy. Understood. I want to verify that a negative energy is "better" than a positive energy, and a more negative energy is "better" still. This is what I assume now, but I had an angst that the energy value is somehow based on absolute value, so the "best" minimized energy is zero. Humor my question, because I have to be 100% certain. No need to go into caveats about the ability of Chimera minimization to make models worse, and how difficult the energy parameter is to interpret. Tom. Thomas W. Sturgill, M.D.-Ph.D. Biozentrum, University of Basel Department of Biochemistry/Hall Lab Klingelbergstrasse 70 CH4056 Basel, Switzerland TEL: (+41 61) 267 2172 FAX: (+41 61 267 2149 Visiting Professor U. of Virginia, Pharmacology Charlottesville, VA 22908 USA FAX: (434) 924-5207

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Display at low definition
by Damien Larivière 20 Dec '12

20 Dec '12

Dear all, I have a basic question: In the image below, on the left, the definition of the atoms is quite good, they are perfect spheres. On the right, they are not anymore. I probably activated something in Chimera, but I'm not able to remember. May you tell me what to do to get a good definition again? Many thanks for your help, Damien

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RNA structure creation plugin
by Eric Pettersen 19 Dec '12

19 Dec '12

Hi All, Dr. Fabrice Jossinet from the University of Strasbourg recently released Assemble2, a Chimera plugin for designing RNA structures in 2D and then generating the corresponding 3D structure. If you're an RNA person, maybe you'd like to try it out and offer feedback. Here's the Assemble2 web site: http://bioinformatics.org/assemble/index.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Adjust bond angle doesn't seem to work
by oxi 19 Dec '12

19 Dec '12

Hi, I'm new to Chimera Using 1.7 candidate build 37955 When I select two adjacent bonds and adjust their relative angle in Tools->Build Structure->Adjust bond angles, nothing seems to actually change in the graphic view I tried selecting the 3 atoms involved afterwards and measure the angle, and it still reports the original angle, so I don't think it's a graphic glitch but the angle isn't actually being changed. Is this a bug or am I doing it wrong? Thanks

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rotation axis display
by Hernando J Sosa 19 Dec '12

19 Dec '12

Hi, Is there a way to display an axis line? I would like to display the rotation and translation axis as given in the reply log after a fit in map operation. Thanks Hernando

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selected molecule
by krit tantanarat 18 Dec '12

18 Dec '12

Dear all I am using MAC and try to select the atom by using Control + left click no mouse but it did not work. How to picking atom from screen using MAC ? Thanks, Krit

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problems with mounted filesystems on MacOS
by Mario Dejung 17 Dec '12

17 Dec '12

Hi everybody, I have a problem with Chimera on my Mac computer. I have a mounted filesystem on my computer, but sometimes (Wifi switched of for example), the path is no longer available and my Chimera crashes, if I try to open a file, because this mounted path is the last one Chimera is trying to open, but the path is no longer available… So Chimera is no longer responding and I have to force quit. The next problem is, when I restart Chimera, it is still trying to open something from the last path… And crashes again. The only thing that works is, I have to double click a map or a pdb or something, but then, when I try to open something with the menu, Chimera is no longer responding. Hope someone has some suggestions and can help me. Thanks in advance Mario

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Electric field lines?
by Hurt, Darrell (NIH/NIAID) [E] 17 Dec '12

17 Dec '12

Hi Chimera team, Is it possible to visualize electric field lines in Chimera from, for example, an APBS run? If so, how do I do it? I've scanned through the documentation, but didn't find anything… Thanks, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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mouse does not report potential values after change of surface transprency
by Boaz Shaanan 15 Dec '12

15 Dec '12

Hi, When I colour a surface according to the potential (read from a delphi or apbs map) and change the surface transparency (in order to show some residues below the surface), the mouse no longer reports the potential values as I walk over the surface. I have to re-colour the surface in order to get back this functionality but the surface is opaque now. Is that how it's supposed to be? Thanks, 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: Friday, December 14, 2012 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 116, Issue 19 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. Re: mask command (Tom Goddard) ---------------------------------------------------------------------- Message: 1 Date: Thu, 13 Dec 2012 16:15:56 -0800 From: Tom Goddard <goddard(a)sonic.net> To: Xiangan Liu <xiangan.liu(a)gmail.com> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] mask command Message-ID: <50CA6FBC.6020202(a)sonic.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Xiangan, The mask command is working fine in my tests. It only sets the map values to zero outside the surface. The values inside the surface are identical to the original map. If that is not the case for you than use menu Help / Report a Bug... and provide the exact mask command you used and explain how you know that the new masked map values are different from the original map. This sounds like the right approach to segmenting a subunit. If instead you had a fit atomic model you could use Color Zone and the Split button on that dialog. Tom > Hi Tom, > I am trying to use your MASK command to extract some interested > volumes from a density map based on another reference density map. > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/mask.html > > I followed your guide line from the link above, but the extracted > density is not the same as the original density. > Is there anything I should pay special attention? > It looks like the command was created many years ago, is it still good > for the latest chimera version? > > Do I have any other way to segment map based on a known subunit > density map, something similar to color zone? > > Thanks, > > Xiangan Liu > > ------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users End of Chimera-users Digest, Vol 116, Issue 19 **********************************************

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Re: [Chimera-users] mask command
by Tom Goddard 14 Dec '12

14 Dec '12

Hi Xiangan, The mask command is working fine in my tests. It only sets the map values to zero outside the surface. The values inside the surface are identical to the original map. If that is not the case for you than use menu Help / Report a Bug... and provide the exact mask command you used and explain how you know that the new masked map values are different from the original map. This sounds like the right approach to segmenting a subunit. If instead you had a fit atomic model you could use Color Zone and the Split button on that dialog. Tom > Hi Tom, > I am trying to use your MASK command to extract some interested > volumes from a density map based on another reference density map. > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/mask.html > > I followed your guide line from the link above, but the extracted > density is not the same as the original density. > Is there anything I should pay special attention? > It looks like the command was created many years ago, is it still good > for the latest chimera version? > > Do I have any other way to segment map based on a known subunit > density map, something similar to color zone? > > Thanks, > > Xiangan Liu > >

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Mac Retina display
by Tom Goddard 14 Dec '12

14 Dec '12

A few weeks ago I added support in Chimera for retina displays (2880x1800 pixels) on Macbook Pro laptops. The recent Chimera builds use the full resolution and produce beautifully smooth edges and text. Older versions of Chimera will use only half the retina screen resolution 1440x900, which is comparable to non-retina displays (~120 dots per inch). The attached image compares the old (left) and new (right) graphics and text in a direct screen snapshot magnified by 2x. The improvement is in Chimera daily builds and the Chimera 1.7 release candidate. Tom

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Saving trajectories in one pdb file
by Daniel Gurnon 13 Dec '12

13 Dec '12

Hi all, I'm using Chimera to prepare multi-model pdbs for use in ePMV. I've run into two issues: 1) When saving a portion of a trajectory in one pdb file, frame numbers are used as model numbers. But only 4 digits are supported. Above 9999, the model number becomes ****. Could you enable 7 digits? I'm taking frames from the end of a long trajectory. 2) I was hoping that I could retain the effect of "hold selection steady" by saving as a pdb with transformed coordinates, but this isn't the case. Is there a way to make this work? Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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morphing model extrapolation
by Gajewski, Stefan 12 Dec '12

12 Dec '12

Hi! I have two .pdb files on hand. Both are in between two biologically relevant conformations. When I create a morph between them, I can see them permuting between the two crystal structures but only half way to the two relevant conformations. The morphing model should generate a trajectory between the two coordinate sets. Is it possible to let the morphing model generate more coordinate files/frames beyond the target structure? Let's say 120 frames morph A to B and compute 60-100 more frames beyond B based on the previous trajectories? Thanks, Stefan ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer

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Measure symmetry helix
by Mariam Shirdel 12 Dec '12

12 Dec '12

Hi! I'm trying to measure the symmetry of an EM density map to fit a pdb to it and make several copies. When I run the commands in the command line: me sym #0 min 0.89 helix 8.97,-111.86, the result I get is Symmetry EMnew.spi: Helix C5, rise 8.97, angle -111.9, center 39 39 38, n 30. The problem is that when I run sym #1 group #0 update true, I get a pentagon base which goes through the whole helix. I just want the measure symmetry to give me Helix, without the C5. What are the commands to achieve this? I tried: sym #1 group c5*h,8.97,-111.86, but it didn't work, and I don't think that's the correct way for me to do it. Does anyone know what to do? Best regards, Mariam Shirdel

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Question about displaying x-ray ribbon.
by Jianfeng Lin 11 Dec '12

11 Dec '12

Hi Chimera Team, Is it possible to make the ribbon of PDB crystal structure plumper in Chimera. I wonder it because the ribbon of interested crystal structure looks slim (in flat, edged, or rounded mode), and leaves much empty space when I fit it into my low resolution cryo-ET volume. Thank you very much in advance! Jianfeng -- Postdoc at Nicastro Lab Biology Department Brandeis University 415 South Street, Waltham, MA 02453, USA Tel. 001-781-736-2439

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model loop in chimera
by Mikolajek H. 11 Dec '12

11 Dec '12

Hi, I am trying to model a protein in chimera using the model loop command. I get this error: Modeller temporary directory: c:\users\admini~1\appdata\local\temp\modellerjtn4xd Unable to run modeller: [Error 2] The system cannot find the file specified Do you know where I am going wrong? Best wishes Halina

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surface calculation
by Anton Vila Sanjurjo 11 Dec '12

11 Dec '12

Hi, I have seen posts regarding this problem before. Here is the log I got after attempting to render a surface representation of the 50S ribosomal subunit (rcsb ID: 3CPW). #0, chain 0: 23S ribosomal rna #0, chain 1: L35E #0, chain 2: 50S ribosomal protein L44E #0, chain 4: 5'-R(*cp*cp*ap*(phe)*(aca))-3' #0, chain 9: 5S ribosomal rna #0, chain A: 50S ribosomal protein L2P #0, chain B: 50S ribosomal protein L3P #0, chain C: 50S ribosomal protein L4P #0, chain D: 50S ribosomal protein L5P #0, chain E: 50S ribosomal protein L6P #0, chain F: 50S ribosomal protein L7AE #0, chain G: HS6 #0, chain H: 50S ribosomal protein L10E #0, chain I: 50S ribosomal protein L13P #0, chain J: HMAL13 #0, chain K: 50S ribosomal protein L15P #0, chain L: 50S ribosomal protein L15E #0, chain M: 50S ribosomal protein LC12 #0, chain N: 50S ribosomal protein L18E #0, chain O: 50S ribosomal protein L19E #0, chain P: 50S ribosomal protein L21E #0, chain Q: HL31 #0, chain R: 50S ribosomal protein L23P #0, chain S: 50S ribosomal protein L24P #0, chain T: 50S ribosomal protein L24E #0, chain U: HL21/HL22 #0, chain V: 50S ribosomal protein L30P #0, chain W: 50S ribosomal protein L31E #0, chain X: 50S ribosomal protein L32E #0, chain Y: HL5 #0, chain Z: 50S ribosomal protein L37E C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface calculation failed, mscalc returned code 5. Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface 3CPW.pdb, category ligand, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 989.35 Total solvent accessible surface area = 1473.85 In this case, I am not interested in splitting the file into its individual chains. I have also unsuccessfully played with the probe-radius and vertex parameters. I should mention that I was able to get this to work with previous versions of Chimera (1.5.something) and that small proteins can be successfully rendered with the latest versions. best, Antón -- Antón Vila-Sanjurjo, PhD Marie Curie fellow Grupo QOSBIOS, Dept. Química Fundamental Facultade de Ciencias Universidade de A Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2659 e-mail: antonvila.s(a)gmail.com

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placing models on the same plane
by Bala subramanian 10 Dec '12

10 Dec '12

Friends, I open two pdb files. When i visualize them, one model is far away from the viewer and another is closer. I want to put both models on the same plane in order to make a figure. Is there any way to do this without doing a fitting. Thanks, Bala -- C. Balasubramanian

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Re: [Chimera-users] [chimera-dev] Hello~ how to make a 3D structure for a number of family genes
by Elaine Meng 10 Dec '12

10 Dec '12

Hi Tao Zhao, Chimera does not do homology modeling directly, but it can connect to a web server running the Modeller program. To use this feature, you would first need to go to the Modeller web site and sign up for a license key <http://www.salilab.org/modeller/registration.html> -- it is free for noncommercial use. A full explanation of homology modeling is not feasible for this mailing list (there are probably several books and thousands of papers on this topic), but for a description of the Modeller interface in Chimera, see: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> ... and for more about how to get the input ready... it sounds like you are "Starting with a structure already known to be a suitable template": <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu…> There is also a tutorial, but be aware that it is only one example, and the process may be different depending on your protein of interest and what is known about it. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html> 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 P.S. better to send questions about using Chimera to chimera-users(a)cgl.ucsf.edu (CC'd on this message), not chimera-dev(a)cgl.ucsf.edu which is meant for programmers On Dec 2, 2012, at 10:21 PM, tao zhao wrote: > Hello, > I am new to chinmera, this tool seems really powerful. Here is my question, I want to build a structure for a number of peptide sequences, all belongs to the AP2 family. > It has one homology NMR model, PDB ID: 1gcc. And I don't know what to do next. > > Could you please give me some instruction? > Thank you very much. > > Tao Zhao > Northwest A&F University,Yangling, China

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