- Chimera-users - RBVI Mailing Lists

clipping and capping
by George Tzotzos 07 Aug '15

07 Aug '15

I’m a real novice in this kind of operation so I shall try in some detail what I’m trying to achieve. I’m dealing with a long serendipitous ligand that spans through a homodimer (2erb) (see screenshot1). I would like to generate something like the B-factor colouring feature (http://www.cgl.ucsf.edu/chimera/features.html <http://www.cgl.ucsf.edu/chimera/features.html>). I’ve opened the Depiction tool and tried surface clipping and capping to no avail. Reading the manual, I figured out that first I have to generate a volume and then use the sop clip command. If this is the routine, I’m seeking advice on how to generate the volume data and then pass it to the sop clip command. As always grateful for your kind help Regards George

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Changing license agreement email
by Flaherty, Daniel P 07 Aug '15

07 Aug '15

Hello, I am using the academic license agreement for Chimera from my previous position at the University of Kansas. However, I have now moved to Purdue and am starting my own laboratory. I would like to utilize Chimera in my lab. I sent an email earlier regarding generating spheres when preparing a protein for docking from my Purdue email and it told me I was not a registered user. I subsequently re-sent the email from my KU email since that is what I was licensed under. Long story short. How to I switch the license agreement to recognize my Purdue email as the registered user? Do I need to un-install Chimera and go through the steps to accept the academic licensing again using my new Purdue email account? Sorry for the confusing email. Thanks! Dan Daniel P. Flaherty, Ph.D. Assistant Professor Department of Medicinal Chemistry and Molecular Pharmacology Purdue University dflaher(a)purdue.edu Office - (765) 494-4761 [cid:8F36A2D2-6664-4FA0-B72D-D785C950B081]

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Placing markers in specific points of an EM map using command line
by Ana Lucia Alvarez Cabrera 07 Aug '15

07 Aug '15

Dear colleagues, I would like to know how can I place markers in specific points within an EM map, using commands (and not the Volume Tracer option in the graphic interface). I am doing a movie and I need to place markers in different regions of a map. By placing the markers first manually with the mouse (using the Volume Tracer option in the graphic interface) into the map and saving the respective marker set I can know the specific coordinates for each marker by reading the output marker file "suffix.cmm" (for example: <marker id="1" x="22.28" y="24.608" z="17.976" r="1" g="0.49804" b="0" radius="2"/> ), but I still don't know how to use this information when writing the command for placing the marker in that position. Thanks in advance, Ana-Lucia

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Re: [Chimera-users] Help Generating Spheres
by Repic Matej 07 Aug '15

07 Aug '15

Dear Daniel, The error you are getting only says that the sphgen program is not in your $PATH and therefore the shell cannot find the executable to run. Make sure you have installed DOCK6, which is not bundled with Chimera. You need to apply for the DOCK6 license (free for academia) and the "sphgen" program will be bundled with it. Apply here: http://dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html After you have made sure DOCK6 is properly installed by following the instructions below, you can follow all the tutorials available online. http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Installation Best, Matej ------------------------------------------------------ Dr. Matej Repic Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational Chemistry and Biochemistry SB - ISIC – LCBC BCH 4108 CH - 1015 Lausanne ------------------------------------------------------ From: <chimera-users-bounces(a)cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu>> on behalf of "Flaherty, Daniel P" <dflaher(a)purdue.edu<mailto:dflaher@purdue.edu>> Date: Friday, August 7, 2015 at 04:38 To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] Help Generating Spheres Hello, I’m teaching myself to perform molecular modeling and docking using your tutorials. I am trying to prepare a protein for a vHTS and I have run into a snag during the sphere generation tutorial (http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_…) In the section where it says,"To generate the spheres, simply use the command "sphgen" in the same folder that contains the INSPH and the rec.ms files. The output will be two files: rec.sph<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/rec.sph>, which contains the spheres in clusters, and OUTSPH<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/OUTSPH>, which contains general information about the calculation.” I am getting an error that says Unrecognized command: “sphgen”. I downloaded the INSPH text file but I have no idea what to do with it. I don’t know what “folder” the tutorial refers to when it says,”use the command ‘sphgen’ in the same folder that contains the INSPH and rec.ms files." Any help would be greatly appreciated! Thanks, Dan

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Help Generating Spheres
by Flaherty, Daniel P 06 Aug '15

06 Aug '15

Hello, I’m teaching myself to perform molecular modeling and docking using your tutorials. I am trying to prepare a protein for a vHTS and I have run into a snag during the sphere generation tutorial (http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_…) In the section where it says,"To generate the spheres, simply use the command "sphgen" in the same folder that contains the INSPH and the rec.ms files. The output will be two files: rec.sph<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/rec.sph>, which contains the spheres in clusters, and OUTSPH<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/OUTSPH>, which contains general information about the calculation.” I am getting an error that says Unrecognized command: “sphgen”. I downloaded the INSPH text file but I have no idea what to do with it. I don’t know what “folder” the tutorial refers to when it says,”use the command ‘sphgen’ in the same folder that contains the INSPH and rec.ms files." Any help would be greatly appreciated! Thanks, Dan

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Morphing with pipes and planks
by Tom Goddard 06 Aug '15

06 Aug '15

Hi Corey, Pipes and planks depictions don’t update when the molecule changes shape. It is also slow to compute so it wouldn’t work interactively. But if you want to make a movie it can be done with some trickery. The tricky part is that there is no command to make the pipes and planks depiction. But a few lines of Python (file updatepp.py attached) can update the pipes and planks. So after creating the morph and the initial pipes and planks I can record a movie with the following command sequence: movie record super 3 ; coordset #2 0,100 ; perframe "open /Users/goddard/ucsf/chimera/libs/PipesAndPlanks/updatepp.py" frames 100 ; wait 100 ; movie encode ~/Desktop/planks.mp4 Tom > On Aug 6, 2015, at 2:35 PM, Corey Dambacher wrote: > > Hi Tom, > > Gabe lander suggested I email you regarding morph maps between two models: > > Is there a way to do a morph using pipes and planks? I have a couple of models I would like to morph, and this works very well when in ribbon, but it doesn't seem to work when I have the pipes and planks depiction... > > Thanks for your time and consideration, > > Corey

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vop cover for maps from EDS server?
by Oliver Clarke 05 Aug '15

05 Aug '15

Hi all, I would like to use the command ‘vop cover’ (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover) with option fbox so that I can easily extend 2fo-fc maps downloaded from the EDS using ‘Fetch by ID’ to cover multiple unit cells. At the moment, this command does not seem to respect the lattice symmetry of the input map (see attached) - is there any way to make it do so? I have tried explicitly specifying the option ‘useSymmetry true’, but it shows the same behaviour. The example PDB ID I used for the attached screenshot was 3CH3. Cheers, Oliver.

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How to find a specific motif from a protein structure?
by Jing Tang 05 Aug '15

05 Aug '15

Hi, I would like to know how to identify a given motif such as DFG in a protein kinase structure. I have thought to use "select: asp,phe,gly" but it found all the residues rather than the motif. A related question would be then how to identify the activation loop or other more specific domains such as p-loop p+1 loop etc. from a structure. Thanks, Jing

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How to record the movie in the main window as well as in the sideview window?
by zhongjun hu 05 Aug '15

05 Aug '15

Hello, Everyone: I want to record the movie of main window as well as the side view window. Until now, I haven't find any simple way. Are there any suggestions or ideas? Thank you so much! Best, Zhongjun Hu 08/05

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opening *cif format
by Dmitry 05 Aug '15

05 Aug '15

Dear Colleagues, I'm trying to open 4fe1-sf.cif file with chimera 1.10.2. But nothing is happening. Although the program saying : "Done opening ....." Could you please explain how to open *cif files ? Sincerely, Dmitry

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