- Chimera-users - RBVI Mailing Lists

Symmetry generation question
by Bala subramanian 29 Oct '13

29 Oct '13

Hello, 1) I have modelled one chain of a multimer. Since this is a modelled structure I dnt have any symmetry information in my pdb. In such case, how can I generate the symmetry related copies. Say I want to apply a fivefold symmetry along z-axis, how can I achieve it ? 2) I used a template structure from PDB to model my structure. What is the correct way to apply the symmetry of existing pdb model to my modeled chain. I tried this as follows, I opened my model as #0 and then the template pdb structure #1 and tried the following sym command and obtained an error as '#0 has no biological unit info.' sym #0 #1 Thanks, Bala -- C. Balasubramanian

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coloring plane by ESP
by Elaine Meng 29 Oct '13

29 Oct '13

Hi Marek, Just thought I'd mention that in Chimera you can color a plane that is in any orientation by the values in an ESP map. Unfortunately it doesn't work with the planes from Axes/Planes/Centroids, but you can create a rectangular plane with specified height and width with command "shape rectangle". Then you can open the molecule and the ESP map, activate/deactivate models (freeze/unfreeze them) and use the mouse to position the rectangle however you like in relationship to the molecule. Then you can use the "Surface Color" tool (aka Electrostatic Surface Coloring) to color the rectangle by the ESP map values. If you didn't already have an ESP map, you could use the PQR and APBS tools in Chimera to calculate one with APBS, or use the Coulombic Surface Coloring tool with option to "Compute grid" (i.e. make ESP map). Attached image is for 3eeb chain B, ESP map file 3eebB.phi ( available from link near bottom of the Surface Properties image tutorial <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> ), and rectangle created with command: shape rectangle height 50 width 50 widthdiv 100 heightdiv 100 center protein It shows the area of strong positive potential near where the highly negatively charged ligand binds. 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

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no moleculr dispay with version 1.8
by Robert Wohlhueter 28 Oct '13

28 Oct '13

I have chimera-1.5.3 running on my Linux-AMD64 Ubuntu (12.10) computer. It works fine in every respect. Recently I installed version 1.8, with runs, but with one fatal flaw. By "runs", I mean the chimera screen comes up, the menus display. If I load (say, a pdb file), it seems to be there in the sense, for example, that I can open and view its sequence. BUT the molecule display window is absolutely blank (black). I suspect it has either to do with my python installation, or with my NVIDIA graphics driver. But whatever the problem, it effects only v. 1.8, not v. 1.5.3. For NVIDIA driver I'm using version 310.14. For python, I understand chimera uses 2.7. My python executable is indeed set as version 2.7.3 (that is, `python --version1 returns 2.7.3), though I have version 3 installed, and it could be used, if needed. I'm not all so clear on how envars PYTHONHOME and PYTHONPATH may or may not effect chimera. Of course, the easy way out is to stick with chimera-1.5.3 -- but one likes to stay up-to-date. Thanks in advance for any profound wisdom. Bob Wohlhueter

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Need help with fit into segment function
by Michael Matho 28 Oct '13

28 Oct '13

Hello, I have an EM map segmented in 5 segments I need to fit 5 molecules into. I'm trying to select a specific segment in order to fit each molecule individually, one after the other. After reading the tutorial, I still cannot figure out how to select only one segment of the map: If I try selecting from "Render/select by attribute" and choose "Segmentation regions" (and I do have the 5 segments ready), only the full map shows up, not the segments! In the "fit to segment" window, I select the molecule to fit and click on Fit... then there's a bug. I'd appreciate your help on how to finalize my fit. Thanks, Michael H. Matho, Ph.D. | Research Associate | Department of Cell Biology La Jolla Institute for Allergy and Immunology 9420 Athena Circle | La Jolla, CA, 92037 Tel: (858) 752-6631 | mmatho(a)liai.org

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Morph movie issue
by Kang, Yanyong 28 Oct '13

28 Oct '13

Dear Chimera developer, I have some problem for making morph movie. My start model has the secondary structure, but the final model loses most of the secondary structure. My morph movie could not show the secondary structure transition of the protein structure. If I change final model as the start model, the start model is as the final model. Secondary structure is the same with the start model. Do you have any ideas to solve this issue? Thank you very much Best, Yanyong Dr. Yanyong Kang Laboratory of Structural Sciences Van Andel Research Institute Tel, 616-234-5446

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rotation of the molecule using plane and the axis ?
by Marek Maly 25 Oct '13

25 Oct '13

Hello, if I define plane "p" using 3 atoms of the given molecule, is there any possibility to rotate consequently molecule into the position in which the chosen axis of the coordinate system (x or y or z) is perpendicular to the plane "p" ? (Of course except slow and not accurate "manual" rotation by mouse). Than you, Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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can get sequence from UniProt website
by Elaine Meng 25 Oct '13

25 Oct '13

Hi Pavithra, I forgot to mention that you could just go to the UniProt web site and save the sequence as a file, then open the file in Chimera. For example, I went to UniProt, searched for oprd_human, then in the Sequences section of the oprd_human page, clicked "FASTA" to get to the URL below, contents of which you can save as plain text file named ending in .fa or .fasta and then open in Chimera with File... Open. <http://www.uniprot.org/uniprot/P41143.fasta> It would not have the annotations mentioned in the comparative modeling tutorial, but those aren't important for doing the tutorial. After opening the FAST file as described above, you can then carry on with the tutorial starting with the fourth paragraph in the "Blast Search for Templates" section ("The next step...". <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html> 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

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chimera in mac osx 10.9
by Pu Qian 25 Oct '13

25 Oct '13

Hi, I upgraded my mac to 10.9 Marvericks. Chimera does not show up input text in Command windows or other text windows properly. I'm using version 1.9, 2013-10-24, 64-bit for mac OSX. It would be a great appreciated if you could tell me which version I should use for this new OSX. Thanks. Best regards Pu Qian The University of Sheffield, UK

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BadStatusLine error
by Pavithra 24 Oct '13

24 Oct '13

Dear chimera users, I'm trying comparative modeling tutorial in chimera tutorials and I'm getting the following error in using fetch uniprot id. *Steps followed: * Menu--> fetch by ID--> selected uniprot--> "oprd_human" "P41143" (tried all combinations) *Error:* *BadStatusLine: '' File "C:\Program Files\Chimera 1.7\bin\lib\httplib.py", line 371, in _read_status raise BadStatusLine(line) See reply log for Python traceback. * I tried changing the preference to use "http" but nothing fix it. please help. -- regards, Pavithra.K.B.

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Typing broken in Mac Mavericks (10.9) with 64-bit Chimera
by Tom Goddard 24 Oct '13

24 Oct '13

With the new Mac operating system Mavericks (Mac OS 10.9), typing into Chimera entry fields is not working in 64-bit Chimera but works correctly in 32-bit Chimera. Also as reported earlier a Mavericks graphics driver bug causes Chimera 1.8 to crash displaying any atoms or bonds. The crashing problem has been fixed in today's Chimera daily build (by disabling an advanced graphics feature automatically on Mac 10.9). So the only Mac Chimera that will work correctly on Mavericks is today's 32-bit daily build (or newer). Tom

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odd surface graphics artifact
by Scott Classen 23 Oct '13

23 Oct '13

Hello, I'm trying to fade a surface to 100 transparent with the following command transparency 100,s #2 frames 30; wait 30 and when the surface goes from 0% transparent to 1% transparent I see the following clipping at the top of the surface: What is causing this and how can I eliminate it? Thanks, Scott

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Chimera crashes on Mac OS 10.9 Mavericks
by Tom Goddard 23 Oct '13

23 Oct '13

For those updating to the newly released Mac operating system Mavericks (10.9), we already have several reports that Chimera crashes showing any molecule due to a graphics driver bug in the new Mac operating system. I suggest not updating to Mavericks immediately if you want Chimera to continue to work. Only Apple can fix this bug. But we will disable the advanced graphics that leads to the crash in tonight's daily build. So if you already updated to Mavericks you can try the Chimera daily build (available about 16 hours after this post) instead of the Chimera 1.8 release. If you want the Chimera 1.8 release to work in Mavericks you'll need to disable DrawElementsInstanced in the Chimera debug graphics driver dialog. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html Disabling this graphics feature (which is what the daily build will do automatically) will cause rendering of large molecules to be slower when atoms are shown as spheres/balls or bonds are shown as cylinders, about 30 times slower. Still it should be as fast as the older Chimera 1.6 version where we did not use this advanced graphics feature at all. Tom

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Problem with Chimera-1.8-linux-x86_64
by Stephen P. Molnar 23 Oct '13

23 Oct '13

I have installed chimera-1.8-linux-x86_64 in VMware Player v-6.0.0 build-1295980 without any waning or error messages. When I start chimera I get the splash screen, then: ./chimera X Error of failed request: BadDrawable (invalid Pixmap or Window parameter) Major opcode of failed request: 72 (X_PutImage) Resource id in failed request: 0x4000064 Serial number of failed request: 1352 Current serial number in output stream: 1358 computation@inga:~/Apps/chimera/bin$ Please advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemisry.com (614)312-7528(c) Skype: smolnar1

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Chimera and Mac Mavericks
by Evan Kantrowitz 23 Oct '13

23 Oct '13

I just install Mavericks on my Mac. Chimera starts OK, but if you try to type into a field, like the PDB fetch field, entering key strokes is very hard. Evan ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------

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hydrophopic interaction
by LU Zen 23 Oct '13

23 Oct '13

Hi All, I have a amphipathic helix/membrane complex assembled with CHARMN-GUI and I'll like to show those residues that come into contact with the lipid bilayer. Using find clash/contact function, I can see many lines joining the atoms of both the residues and lipid bilayer. However, I don't really know how to pick the true hydrophopic interaction from the rest of the clashes/contacts. In addition, is there a way to quatify which these interactions may be tighter than the other. Any suggestion is appreciated. Thanks, ZL -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Create a protein model using Chimera?
by Maja Divjak 18 Oct '13

18 Oct '13

Hello Chimera, I have looked high and low for the propeptide domain of IL-1 beta, but it does not exist as a PDB. I was therefore wondering what is the best approach to generating a 3d structure for the propeptide domain using the protein sequence and Chimera? If you could please outline a possible process, I would very much appreciate it. I see you have tutorials for comparative modeling, but in this case there is nothing to compare it to except other homologous sequences from the IL-1 family. I look forward to your reply! Thank you and best wishes, Dr Maja Divjak, WEHI, Melbourne, Australia ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________

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Re: [Chimera-users] Cross-section question
by Tom Goddard 18 Oct '13

18 Oct '13

Hi Lawrence, Sure it is easy to see plane 72. Use the Volume Viewer dialog, show the planes panel (menu Features / Planes), press the "One" plane button in that panel and set the plane number entry field to 72. To assure you see the full resolution data make sure "Step" is set to 1 above the volume dialog density map histogram, and that "depth" is set to 1 in the Planes panel. This and other Chimera density map features are described in the Chimera guide to volume data display http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html Tom On Oct 18, 2013, at 10:09 AM, "Tartaglia,Lawrence J" wrote: > Hi Tom, > > Thank you for getting back to me. I should have been a bit more clear. What I want is the exact "central" section. I'm not sure if you are familiar with cryo-electron microscopy? I used a box size of 143 pixels to box my virus particles. What I would like to see if image 72 (central section) of my reconstruction. Is there a way to do that? I've attached an image of an example central section (left hand side) using the program IMOD. I'm sorry for the confusion... > > Best, > > Lawrence > > > On Thu, 17 Oct 2013 09:43:43 -0700, Tom Goddard wrote: >> Hi Lawrence, >> >> I'm not sure what you mean by "exact cross-section". Do you mean >> aligned to the virus map grid axes? If so the Orient button at the >> bottom of the volume viewer dialog will do that. But probably it is >> better to simply specify which planes to show using the Region Bounds >> panel of the volume viewer dialog (Features menu) - specify a z range >> 120 125 1 to show planes 120 to 125 using step 1 (i.e. every plane). >> This will be better than using clip planes. >> >> Tom >> >> >> On Oct 16, 2013, at 11:35 AM, "Tartaglia,Lawrence J" wrote: >> >>> Hello, >>> >>> I have a cryoEM map of a virus that I'm visualizing in chimera. I'd like to get a perfect cross-section of the map that I can use for publication. I've used the "side view" tool, but I can't get an exact cross-section. Are there any options to achieve this? >>> >>> Thanks! >>> >>> Best, >>> >>> Lawrence >>> -- >>> Lawrence J. Tartaglia, Ph.D. >>> Postdoctoral Scientist >>> Agbandje-McKenna Lab >>> Department of Biochemistry and Molecular Biology >>> College of Medicine, University of Florida >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> > > -- > Lawrence J. Tartaglia, Ph.D. > Postdoctoral Scientist > Agbandje-McKenna Lab > Department of Biochemistry and Molecular Biology > College of Medicine, University of Florida<Screenshot-1.png>

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Cross-section question
by Tartaglia,Lawrence J 17 Oct '13

17 Oct '13

Hello, I have a cryoEM map of a virus that I'm visualizing in chimera. I'd like to get a perfect cross-section of the map that I can use for publication. I've used the "side view" tool, but I can't get an exact cross-section. Are there any options to achieve this? Thanks! Best, Lawrence -- Lawrence J. Tartaglia, Ph.D. Postdoctoral Scientist Agbandje-McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine, University of Florida

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Normal to the plane of the aromatic ring at the centroid
by Pande, Ajay K 16 Oct '13

16 Oct '13

How would I draw a normal to the plane of an aromatic ring, at its centroid? Thanks Ajay Pande

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(no subject)
by edward el chamy 15 Oct '13

15 Oct '13

Hey i am a student using chimera 1.8 i have a question: how we find on a specific chain the different interaction domains? Thanks a lot

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Fwd: setting or hardware problem?
by Chao Wang 14 Oct '13

14 Oct '13

Hi, chimera users I am starting to use ucsf chimera to analysis protein structure recently. It is an excellent software, and I have no problem using it at school. But when I try to use it on my other pc at home. It doesn't work properly. The ribbon looks flat and dull, not a 3D looking anymore, like the situation showed in pic1 and pic2. My hardwares: School PC: win7 64 bit,cpu E5-1606, Nvidia Quadro 5000, 4G Home PC: win7 64 bit, cpu i5-2500k, AMD Radeon HD6700, 8G I know the video card of school's pc is much better, but I checked the hardware list. HD6700 is also compatible. Can anyone tell me what is wrong? I really appreciate it. [image: Inline image 1] [image: Inline image 1] Jack Wang

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Chimera commands to record MD movies
by psu4＠uic.edu 11 Oct '13

11 Oct '13

Dear Chimera, Since we run a lot of Amber MD simulation in remote clusters, we wonder if there is any Chimera command that can record the Amber MD trajectories remotely and save them as avi (or any other movie file formats)? If this is feasible, then we don't have to download all the trajectories to local and make the trajectory movies manually. We have searched the Chimera user manual but didn't see any command. If there are related commands which we didn't see, please forgive us : ) Thanks. * There is a way to activate X11 forwarding and use remote Chimera GUI to do this, but it's extremely slow and prone to freeze the computer. Cheers, Henry

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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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Packaging sessions
by Amedee des Georges 08 Oct '13

08 Oct '13

Dear Chimera, Currently, Session saves don't save volume data, only link to them, which is an issue whenever one of those links is broken or when one wants to send a whole session to someone else. Would it be possible to have an additional saving option that could be called "Package session" (like in InDesign), where a folder is created and all the files associated to the session saved in it. This way, people could zip and send the package by email, or package their important sessions to make sure not to lose them, or just to move them around. By advance, many thanks, Amedee -- Amedee des Georges Frank lab Howard Hughes Medical Institute Dept. of Biochemistry and Molecular Biophysics 650 W 168th St, P&S Black Building room 221 New York, NY 10032 (T) 212 305-9527 (F) 212 305-9500 (E) ad2720(a)columbia.edu http://franklab.cpmc.columbia.edu

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want to converge 20 pdb files of a trimer
by ashok rout 07 Oct '13

07 Oct '13

Hi, I have a nmr structure of a protein which is a trimer. I want to converge 20 pdb files of the trimer, by Chimera. And also want to converge a specific region of the 20 pdb files of the trimer. Can you please assist me how to do this?? Thanks, Ashok -- thanks & regards, Ashok

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