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repeat question
by A G Szabo 10 May '16

10 May '16

I am trying to make the sphere of an ion in an active site larger than what appears in the structure. I asked a similar question back in December, and on checking my notes I tried to use the command setattr ballScale 0.5 I first selected the ion using control<click). The ion was selected. I then tried the command line as I show it above. Nothing appeared to happen. Indeed I tried to do the same for an atom of a residue that I had selected using control <click> again nothing. I must have forgotten something. A message from Elaine suggested that I use setattr m ballScale 0.5 Am I supposed to select the residue and leave out the m? Thanks for your patience. Arthur Szabo

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opengl error with quadro k620
by Krishnan, Raman 10 May '16

10 May '16

[cid:image001.jpg@01D1A9F2.DB70AF30] Get this error on running chimera -debug-opengl option. Using quadrok620 nvidia card on windows 7.0 thanks Director Structural Biology, Biocryst Pharmaceuticals.

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rainbow color scheme
by Shreeramesh 09 May '16

09 May '16

Dear Sir, I guess blue represents N-terminal of protein in rainbow coloring and would like know the indication of other colors in rainbow scheme of chimera for protein structure. Thanks & regards *Ramesh M* Email: shreeramesh(a)gmail.com Mobile: (91) + 9646469938 (27) + (0) 844556164

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I get this when i tried to start chimera 1.11rc on windows 7. any suggestions?
by Krishnan, Raman 09 May '16

09 May '16

[cid:image001.jpg@01D1A55D.8C415B10] krish Biocryst Pharmaceuticals.

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Re: [Chimera-users] [chimera-dev] suggestions for better STL export - remove internal, reduce atom vertices
by Tom Goddard 09 May '16

09 May '16

Hi Jakob, We discussed the excessive STL vertices in atoms and bonds last week and I put a fix into the daily build and release candidate. http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012134.html Apparently you are not using those versions since your images show the high vertex density. I’ve attached an image using the current Chimera release candidate that shows reasonable vertex density. Unfortunately eliminating internal structures and stitching together meshes for atoms, bonds and ribbons at the seams is very difficult. Yes $10000 CAD software packages can do it but we don’t have the resources to solve that problem. Since every 3d printer has to deal with this problem I expect the printer software to be able to handle it, but perhaps it is too hard a problem for the 3d printer companies as well. Perhaps there is free software that can eliminate internal structures and stitch mesh intersecting edges together, I have not researched it — I’d start looking at MeshLab. Tom > On Apr 15, 2016, at 4:33 AM, Jakob Suckale wrote: > > Dear Chimera developers, > > Chimera has the great feature of STL export, very useful for 3D printing models for research and teaching. May I make two suggestion to improve this feature even further. > > > 1 - Remove invisible internal and therefore unnecessary structures. > > Chimera generates a lot of internal structures that complicate printing and are pointless for STLs. This includes inside surfaces at the end of ribbon cartoons (red below). > <Screen Shot 2016-04-15 at 13.24.44.png> > as well as copious amounts of invisible internal surfaces for wire and ball and stick models. > <Screen Shot 2016-04-15 at 13.27.36.png> > If these were automatically removed, STLs would not only be much smaller but also much easier to print without remashing. > > > 2 - Reduce the number of vertices for atom models. > > Ribbon conversion to vertices is already good, but as can bee seen above atom models are converted using far too many vertices inflating the resulting STL files. I'm aware that this has been discussed and listed previously as a bug but the problem remains and makes for difficult to use STLs and bad 3D prints. > > Best regards, > > > Jakob Suckale, PhD > Lecturer in Biochemistry > University of Tübingen > +49-7071-29-73363 > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Alter both clipping planes at same time?
by Oliver Clarke 05 May '16

05 May '16

Hi, is there any way to alter both global clipping planes at the same time? This is handy to move the current viewable section, without altering its thickness. At the moment I use an alias for this: # move both clip planes hither or yon. # Usage: zslab x # Move hither and yon clip planes towards (positive) or away (negative) alias ^zslab clip hither $1; clip yon $1 This works fine, except when the clip planes are close together - in that case, I get an error stating that I'm trying to move the near clip plane behind the far clip plane. It would be nice to have an option to move both planes at once - e.g. maybe changing the syntax of clip so either hither, yon, or both can be specified in the same command would be possible? Cheers, Oliver.

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ImportError: No module named Chimera
by Eiros Zamora, Juan 04 May '16

04 May '16

Hi, I’m running a per-frame script to display the time in a MD movie. I used to run it without problems until I downloaded the new Mac OS X 64-bit 1.11 version. (I erased the old app, also tried to re-download the old version with no success). More specifically, I load the MD movie, and in the command line I write: 2dlabels create timer text "0 ns" color white ypos .9 xpos .9 size 50 then I open a per-frame script with the following commands: from Chimera import runCommand runCommand("2dlabels change timer text '%.1f ns'" % (mdInfo['frame']*0.02)) and get the error: Problem in per-frame script: ImportError: No module named Chimera I’ve googled it and found this reply: [Chimera-users] How to install chimera as a python module http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-July/010120.html I’ve tried setting the $CHIMERA_PATH environment variable to /Applications/Chimera.app/Contents/Resources/share but I still run into the same problem. Now, I don’t want to run the script directly from the command line, as it’s a per-frame script I have to run after I load the MD movie and create the 2dlabel object. Anything obvious I’m missing here? Cheers Juan

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how to move the model and save as mrc
by rongjian li 04 May '16

04 May '16

Hi, I am trying to move the model/protein in some MRC file and save it as a new MRC file. I know how to do it in Windows by clicking the mouse, but I have lots of such operations expected. So I am wondering how could I realize this in Linux such that it can be done automatically. Thank you very much. Best, Rongjian

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Multiple Docking Using Chimera
by SOBAHY, TURKI MOHAMMED 02 May '16

02 May '16

Hello, I have a protein of interest that I need to perform molecular docking on by multiple ligands (~1000,000). The protein is in PDB file format, while ligands are in a SDF file format. Initially, the ligands were divided into multiple SDF files (mini) for hardware sake. Then, a python script was developed to handle the docking of each mini SDF file against the protein of interest. This works nicely, however docking scores (tables) have no ligands IDs associated to distinguish each score. So, basically I have scoring tables without any key IDs!! Kindly, I want to know if you have encountered the same problem and what approach you took to solve this. Thanks,? ______________________________ Turki Sobahy Research Associate Research Center (J-04) King Faisal Specialist Hospital & Research Center (Gen.Org.)-Jeddah Branch PO Box 40047, Jeddah 21499, Saudi Arabia Tel# +966 667 7777 ext. 66736| MCD# 40716 Mobile# +966 505837027 email tsobahy(a)kfshrc.edu.sa<mailto:ESan-Diego@kfshrc.edu.sa>

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Solicitud Información
by luz Martinez 02 May '16

02 May '16

Cordial Saludo Soy estudiante de licenciatura en Química de la UNIVERSIDAD PEDAGOGICA NACIONAL. Colombia, Cordialmente solicito información acerca del modelo matemático general que el programa UCSF Chimera utiliza, lo anterior con el fin llevar a cabo una investigación en el espacio académico de Química Computacional que curso. Agradezco la atención y pronta respuesta Luz Angela Martinez M. Estudiante Decimo semestre

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