- Chimera-users - RBVI Mailing Lists

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 19 Oct '13

19 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 17 Oct '13

17 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 09 Oct '13

09 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 08 Oct '13

08 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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Structural Allignment in Chimera
by Syeda Hira Batool 06 Oct '13

06 Oct '13

Hello I want to know how chimera does Structural allignment. I am writing a python script to allign protein structures(from MD simulations) and eventually calculate RMSD. Please can anyone provide me a source code or a helping material.Thanx in advance. Hira Batool Student of BS-Bioinformatics Biosciences Department COMSATS Institute of Information Technology Islamabad, PAKISTAN

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info pivotting on a single atom
by Christian Martinoli 04 Oct '13

04 Oct '13

dear all, I have troubles in setting the center of rotation on a single atom of my model. i'm working with the command line to build up a short clip at the end.what i would need is pivotting the whole model on the three axes, rather than in 2D as seems work with cofr command. any help? Thanks in advance Christian -- Christian Martinoli University Of Pavia Dept. of Biology and Biotechnology "Lazzaro Spallanzani" Structural Biology Lab. Via Ferrata 1, 27100 Pavia Italy

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command line to define a plane
by Jean Didier Pie Marechal 03 Oct '13

03 Oct '13

Dear all, is there a way to define a plane from the command line. Something that would work providing a list of atoms or a selection. Cheers, JD Dr. Jean-Didier Maréchal Associate Professor The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es

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Re: [Chimera-users] Question about multi align viewer
by Elaine Meng 03 Oct '13

03 Oct '13

On Sep 20, 2013, at 9:33 AM, Sean Connell wrote: > Hello I was wondering if it is possible to calculate conservation statistics using only subsets of the aligned sequence. The reason I ask is that in my alignment I have differently families of proteins that have slightly different functions and I would like to highlight residues that are conserved in one subset but not in the other? > Hi Sean, Not directly. I believe you would have to create alignments of just those subsets. You could do that with some other program (including text-editor) before opening the alignment in Chimera, or you could do it in Chimera. Of course, keep the original file with the full alignment too! To edit in Chimera, open the full alignment and then from the sequence window menu choose "Edit... Delete Sequences/Gaps" and in the resulting dialog, choose which sequences to delete. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> You can then continue working with the subset alignment in Chimera, including saving it to a new file (sequence window menu "File... Save As"). 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. your original message was in an attachment, which was kind of weird, but I could view it by just clicking the attachment

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Stereoscope viewing
by Thompson, Matthew K 02 Oct '13

02 Oct '13

Can anyone recommend the best camera settings for stereoscope glasses? Mine just don't seem to turn out right.

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electrostatic surface calculation
by Ursula Schulze-Gahmen 02 Oct '13

02 Oct '13

I calculated the coulombic surface and the electrostatic surface for my molecule. They show a significant difference in the shape of a small surface area. For the electrostatic surface, I converted the pdb file into a pqr file using the pdb2pqr called from chimera. Then I ran APBS also from within Chimera. When I display this surface it exhibits a strong protrusion in an area where there is no side chain. This protrusion is not present in the Coulombic surface. Any idea where this is coming from? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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how to write script that can run chemera command
by 张海平 30 Sep '13

30 Sep '13

Dear professor: I find a command "delete ligand" can delete ligand from a protein. Then I have thousands of protein contain ligands, how can I write a script to do this command automotically, Thanks for your kindly help. Best regard Haiping Zhang

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Editing Question
by Kirk Moldoff 30 Sep '13

30 Sep '13

Hi, I'm working with a pdb model 3ALQ. It is a Tumor Necrosis Factor and its TNFR receptor. I'd like to be able to turn off the bound TNF. Or select it for deletion. Can't figure how to do this. Any suggestions? Ultimately I'd like to be able to save just the TNFR as a .pdb file. Thanks, Kirk -------- Kirk Moldoff www.galeriekirk.com 609-252-9479

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Generating a PDB file
by Nathalia Varejão 27 Sep '13

27 Sep '13

To whom it may concern, I'm using the chimera to visualize a protein ligand docking, but I want to save the best model as a PDB file that I can use anywhere to perform other analysis, is it possible? For example, the pdb that I saved by the chimera do not open in PyMol viewer... Can you help me? Nathalia

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