- Chimera-users - RBVI Mailing Lists

Group cylinder with a PDB and fit together
by Mario Dejung 07 Nov '13

07 Nov '13

Hi all, I created a some cylinders in chimera to visualise the symmetry axis and the rotation center of a hexametric structure. Is there a way to fix the position of these cylinders relative to the pdb structure? So when I fit the structure, the cylinders will also rotate in the same way. And, by the way, is it possible to duplicate these cylinders, or do I have to create a .bild file and import it several times? Thanks for your feedback. Mario

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How to change the default color for pseudobonds?
by Oliver Clarke 06 Nov '13

06 Nov '13

Greetings, Is there any way to change the default color for pseudo bonds (e.g. distance monitors)? I generally work on a white background, and the default of yellow is very difficult to see. Pretty much everything else in the Chimera GUI seems to be customizable, which I love, but I can’t see how to alter the default in this particular instance. Many thanks, Oliver.

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Specifc silouhettes
by m.maletta＠nki.nl 05 Nov '13

05 Nov '13

Dear All I have docked an X-ray model inside an EM density (mrc). I would like to visualize the density (mrc) with the silhouettes option on and pdb file with the silhouettes option off. Is this possible? Best Max __________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta(a)nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029

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chimera scalability on irix
by tyrrell t 04 Nov '13

04 Nov '13

I couldn't find any information on the subject, and have no hardware to test at the moment, but for a future deployment I need to work with IRIX systems, and I was wondering if chimera is coded to take advantage of multiple MIPS CPUs, or is it strictly a CPU-bound application? ie: would it run better on a dual-cpu octane system at 600mhz, or a 700mhz uni-processor fuel system? ( or something along this line )

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calculate axes from centroids
by Elaine Meng 04 Nov '13

04 Nov '13

On Nov 3, 2013, at 7:49 PM, Lili Peng <lilipeng(a)gmail.com> wrote: > Hi Elaine, > I've inquired you in the past regarding defining angles and planes in UCSF Chimera. > Do you know if there's a way to define an axis through two centroids, or through the center-of-mass of a residue and the centroid of a subunit, some combination like that? > Thank you, > Lili > Hi Lili, Currently, axes (and planes and centroids) can only be calculated from sets of atoms, not centroids. However, it can done in current Chimera by defining centroids, adding fake atoms at their positions, and using those atoms to define axes. You can specify whether each centroid calculation is mass-weighted (center of mass) or not (default, center of geometry). (a) use Axes/Planes/Centroids (or command "define") to define the desired centroids (b) look in Reply Log for the coordinates of each centroid ( c) add atoms: Tools… Structure Editing… Build Structure, Start Structure section, use settings to add atom with specific x,y,z coordinates to the existing model (the one whose atoms you used to define centroid) (d) use new atoms to define axis <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> There is also a "measure center" command that will automatically create a fake atom (option "mark true"), so you could use that instead for steps a-c, but it always does mass-weighting. For non-mass-weighted centroids, you would need to use the full process outlined above. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center> I hope this helps. Sorry it is not as simple as it should be. 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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Fitting models into density - meaning of values
by Jessica Holien 30 Oct '13

30 Oct '13

I have been using Chimera to fit some homology models into the EM density (23A resolution) of a large complex. Although by eye it looks good I am trying to work out if statistically it is good. Can anyone tell me what is a good "Average Map Value" and what is a bad one? Thanks

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Coloring distance lines between atoms
by Tom Goddard 30 Oct '13

30 Oct '13

Hi Damien, Here is a Chimera Python script colordist.py that lets you color distance lines between atoms based on how long the distance is. The colors update as you move one model relative to another. After showing some distances, for instance with the "distance" command you would use command runscript colordist.py 8.5 green red to color the distance lines less than 8.5 Angstroms green, and longer ones red. The script needs to be in the directory you started Chimera in (e.g. on Linux), or you can specify a full path to the script "runscript /Users/Smith/colordist.py …", or use the Chimera "cd" command to change to the directory containing the script. You can select specific distance lines to color with the mouse and use runscript colordist.py 8.5 green red sel You can stop the color updating using runscript colordist.py or for just selected distance lines runscript colordist.py sel Tom On Oct 24, 2013, at 3:13 AM, Damien Larivière wrote: > Hi Tom, > > So, here is a reminder for the script we talked about. > > The idea is as follows: > > Once I have loaded several proteins in Chimera, once I have calculated distances between residue pairs that are displayed in the distance popup window, once I have displayed visually the distance as a colored stick pseudobond, then I would like a switch of the pseudobond color to occur when the distance is higher than a given value as I'm moving the proteins. > So, in my current manual modeling, I'm calculating a total of 24 distances between 5 proteins, I ask Chimera to display 24 pseudobond, most of them are initially let'say red, I load the script after having editing it with the distances and the associated maximal values, I move the proteins and the pseudobond color turn from red to yellow when the distance get lower than the maximal value defined for this distance in the script. And inversely, a pseudobond turns to red from yellow when it gets higher than a maximum distance. > > Let me know if you need more explanations. > > Many thanks for your help, > > Damien >

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color a small molecule in a .mol2 file by red to blue gradient of the partial charges
by Francois Berenger 30 Oct '13

30 Oct '13

Is it possible to do this in Chimera? I'd like a white background too. Thanks a lot, F.

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how to make the background of Chimera-generated images transparent
by Gea-Ny Tseng/FS/VCU 30 Oct '13

30 Oct '13

Dear Chimera developers and users: I would like to know how to make the background of Chimera-generated images transparent. I used to be able to do this with an older version of Chimera. But with Chimera 1.8, I could not figure out how to do this. There are options in the 'Color/Background' to adjust 'Opacity', which to me means that I could make the background transparent by using 'zero'. But this did not happen. Could you please advise? Thank you. Gea-Ny Tseng, PhD Dept of Physiology & Biophysics Virginia Commonwealth University

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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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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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STL file questions
by David Gene Morgan 26 Sep '13

26 Sep '13

Hi, I have a couple of questions about the chimera STL files. I tried to open one using chimera to determine whether they contain any color information, but I wasn't able to open the file I just wrote. I don't care about that, but I would like to know if they contain color information. Is there any way to control the degree of tesselation when writing an STL file? In other words, some STL files are huge because they contain huge numbers of triangles (and some 3d printers can't handle overly large files). I am wondering whether it is possible to control the size of the output files, which is effectively asking if it is possible to control the number of triangles in the file, how finely sampled the model is, etc. (however one wants to describe that property). Finally, as I understand STL files, they are usually "unscaled" (i.e., the co-ordinate system describing the vertices of the triangles doesn't have fixed length units). Is that true for the STL files chimera creates? If I wanted to create two models with an accurate reflection of their relative atomic sizes, are there tricks I will need to employ? -- David Gene Morgan Electron Microscopy Center 320C Simon Hall IU Bloomington 812 856 1457 (office) 812 856 3221 (3200) http://bio.indiana.edu/~cryo

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Calculating SAS areas for selected residues for a whole trajectory of structures
by Harald Lanig 24 Sep '13

24 Sep '13

Dear Chimera users, I am currently using chimera to calculate the solvent accessible surface for several selected residues of a single structure (I am using the Attribute calculator with the formula sum(atom.areaSAS) to do this). Is there a way to apply this to a set of structures coming from a molecular dynamics trajectory? I am interested in how the solvent accessible surface of a set of residues changes during the simulation. Any hint is highly appreciated! Best wishes, -Harald -- ------------------------------------------------------------------------ PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 harald DOT lanig AT fau.de Fax +49(0)9131-85 26565 http://www.chemie.uni-erlangen.de/lanig ------------------------------------------------------------------------

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Building DNA along A PBD Using RNA command
by Joshua Carter 23 Sep '13

23 Sep '13

Hi, I'm working on a project in chimera that involves modeling the binding of a RNA-guided protein complex to a double stranded piece of DNA. What I need to do is be able to is either match a DNA pdb to the existing RNA pdb I have or build one using the rna command in chimera. I know there is a path command, is there any way I could specify that to build along a pdb I have already? Or am I just barking up the wrong tree entirely? Thanks,Josh

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Question about multi align viewer
by Sean Connell 20 Sep '13

20 Sep '13

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selecting a specific residue
by Elaine Meng 19 Sep '13

19 Sep '13

On Sep 18, 2013, at 8:53 PM, Serina Doolittle <serinadoolittle(a)me.com> wrote: > Hi again, > > So now i have another question... > I have selected the ligand because that is what my research mentor and I are interested in (the active site and ligand binding etc.) however, when i select "ligand" it also high lights other molecules around the protein, more around the surface, like butanol - how can i just select the ligand NADPH and not have to select the other small molecule ligands that are not part of the active site of the protein? can i do that? > > Serina Doolittle > Thanks! > Hi Serina, The "ligand" detection uses automatic rules and won't always get what you expect, but there are many other ways to select a specific residue. For example, you can select by residue name and/or number, or with the mouse in the Chimera window. With mouse: Ctrl-click on some atom selects it, and then keyboard up arrow will promote the selection to the whole residue. With command: specify residue name or number, e.g. select :nad select :254.a … would select residue named NAD, or residue 254 in chain A respectively. How do you find out the residue name or number? One way is by hovering the mouse over some atom or bond in the residue, which will pop up a balloon that shows atom name, residue name, and residue number. With menu: Select… Residue… allows selecting by name (all the residue names present will be listed in the menu). NADPH might have residue name NAP, NAD or something like that, since PDB files have 3-letter residue names. That would select all residues of that type, so you'd probably want to use one of the other methods if there are multiple NADPH molecules and you only wanted to select a particular one. Manual pages on selection and command-line atom specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> Also, you may want to look through the "getting started" tutorial to become more familiar with Chimera. <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.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

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Hello
by A Amiri 19 Sep '13

19 Sep '13

Hello. I have a problem with chimera! i want to join two pdb file together by C-N peptide bond. Actually this is a modeling of a fusion protein that one part of its, is a protein and another part is a linker. I need a complete structure. I select the carbon atom from one model and nitrogen atom from another model. I use the "build structure<join modesl" menu for this purpose but the "apply" button is inactive still and i don't know how i can activate it! please help me. ________________________________

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Re: [Chimera-users] vop cover
by Elaine Meng 18 Sep '13

18 Sep '13

Hi Pradeep, That message is saying you must specify the density map. I.e. if the atomic structure is model #0 and the density map is model #1, the command could be something like vop cover #1 atom #0 Command usage and options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover> 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. it is recommended you send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of to me directly - thanks! On Sep 18, 2013, at 2:02 PM, Pradeep Pallan wrote: > Hi Elaine, > > I was looking at using vop cover. I have a case where part of the molecule > is not within electron density box. The map cuts off at the unit cell dimensions, > and my space group is P1. Where I need edensity is approximately at y= -10. > When I try the command > 'vop cover "atom"', it gives the message "file.pdb is not a volume". > > Is this the right way of getting the molecule covered in e density or do I need > to use a different option. > > Thank you, > PP

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