August 2015 - Chimera-users - RBVI Mailing Lists

Attribute "distance" generated by shortcut "ac sd" not saved between sessions?
by Oliver Clarke 10 Aug '15

10 Aug '15

Hi all, I use the command “ac sd” to color dotted surfaces such as the attached by pore radius (I generate a molmap surface corresponding to the channel axis and then use "ac sd" to generate an attribute “distance", which in this case corresponds to the pore radius, which I can then use to color the dotted surface pdb using Render by Attribute). The dotted surface is generated using the program HOLE (http://www.smartsci.uk/hole/) along with the attached script to make it readable by chimera. This all works fine, however I have noted that the attribute generated by "ac sd” is not present when I reload the saved session, whereas other attributes (e.g. those created explicitly with defattr) are. I can just regenerate it of course, but it would be convenient if it were saved with the session, as it can take a while (~10 minutes) to calculate for large dotted surfaces. Cheers, Oliver.

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A video of 'view dock'
by Amali Guruge 10 Aug '15

10 Aug '15

Dear All, Can we save the movie play in 'view dock' option? Can anyone help me? Thank you.

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Re: [Chimera-users] PDB: 3NZ4 (Chimera vs Pmol Visualization)
by Elaine Meng 07 Aug '15

07 Aug '15

Hi Kevin, What you are seeing is weird-looking bonds between the ribbon and the residues named MDO. It is an artifact caused by the default smoothing of the ribbon path, the amino acid derivation of MDO, and the default hiding of “backbone” atoms in Chimera when the ribbon is displayed. More on that here, if anybody wants details... <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo…> As you found, you could just show atoms without ribbons to solve the problem. However, if you really wanted to show ribbons at the same time, here are some choices as to what you could do in Chimera to make it look less deformed: (1) enable display of all atoms of the MDO at the same time as the ribbon, for example with command: ribbackbone .. however, side effects you may not like are that this will also show backbone atoms of the other residues that are displayed, and MDO and these other residues may be obviously detached (as if “floating” away) from the smoothed ribbon. You could try hiding the backbone atoms of the other residues with: ~disp @n,c,o & ~:mdo … or you could go back to the original behavior of disabling simultaneous backbone-atom and ribbon display with: ~ribbackbone (2) use a non-smoothed ribbon path that is forced to go through the CA atoms, for example with command: ribspline cardinal … however, this is still ugly because the ribbon makes a sharp turn near this derived residue, and the methyl group comes off of the ribbon at a strange angle. You can go back to the default ribbon path with: ribspline b Sorry, neither makes a beautiful picture. But I hope this helps to explain what is going on. 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 Pictures before and after using “ribbackbone” command:

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PDB: 3NZ4 (Chimera vs Pmol Visualization)
by Kevin D. Walker 07 Aug '15

07 Aug '15

A specialized prosthesis within the PDB 3NZ4 structure looks proper in Pmol but looks skewed in Chimera (my choice), and I wonder why the prosthesis is rendered as such in Chimera? Kevin ---------------------------------- Kevin D Walker Associate Professor Michigan State University Department of Chemistry and Department of Biochemistry & Molecular Biology 578 S Shaw Lane; Room 208 East Lansing, MI 48824 Phone: 517 355 9715 x 257 Fax: 517 353 1793 websites: 1) http://bmb.natsci.msu.edu/about/directory/faculty/kevin-d-walker/current-re…

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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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Chimera-users August 2015