- Chimera-users - RBVI Mailing Lists

solid threshold in a python script
by benoit.zuber＠ana.unibe.ch 14 Dec '15

14 Dec '15

Hello I would like to add several threshold markers for volume solid rendering. I would like to do it in a script. I guess the only way is to do it through a python script. I tried modifying the solid_levels and solid_colors attributes of the active volume but I could not find how I can then get the depending volume attributes, such as transfer_function and the gui (both rendered volume and the volume viewer dialog) to be correctly updated. Could anyone please give me a few pointers? Thanks in advance Ben -- Prof. Benoît Zuber Institute of Anatomy University of Bern Baltzerstrasse 2<x-apple-data-detectors://1> Postfach 922<x-apple-data-detectors://2/0> 3000 Bern<x-apple-data-detectors://2/0> 9 Switzerland benoit.zuber(a)ana.unibe.ch<mailto:benoit.zuber@ana.unibe.ch> +41 31 631 84 40<tel:+41%2031%20631%2084%2040> http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html

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on preset interactive 1 color
by Smith Liu 12 Dec '15

12 Dec '15

Dear All, If by chimera we select preset interactive 1 for a protein complex, each chain will take a different color. As for when we describe the corresponding colors in a paper we need to know the names of each color by the chimera preset interactive 1 function, and the colors by this function are usualy very close to each other, will you please introduce to me the color names colored by the function preset interactive 1? Smith

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Movie Making in Chimera
by Florian Drechsler 10 Dec '15

10 Dec '15

Dear Chimera Support Team, I have a question regarding movie making in Chimera: I would like to be able to record a movie, based on a chimera script, and have exact frame-wise control over what is recorded. Chimera seems to make a funny distinction between "internal trajectory frames" and "movie frames" which I don't get. I would like a one-to-one correspondence between these, no interpolation or anything like that. More precisely, I would like to be able to do the following, in strict sequential order: - Load some models, - rotate one of the models, - move one of the models, - capture a movie frame of the resulting configuration, and again - rotate one of the models, - move one of the models, - capture a movie frame of the resulting configuration, etc. I have tried using "perframe" commands, where each perframe operation comprises a "move" and a "turn" command, and has the option "frames 1". Still, I don't get exactly what I want: the resulting movie doesn't consist of the number of frames I'd expect - movie encoding seems to start before all commands have actually been executed. I can see a message saying that the movie has been finished, while things are still moving. I've provided a code snippet below. Moreover, rather than using "perframe", surely there must be a more elegant and natural way of enforcing sequential execution of commands, as one would expect from any normal programming language. Thank you very much in advance for your help, Best regards, Florian Drechsler -------------------------- Florian Drechsler Universität Ulm Institut für Biophysik Albert-Einstein-Allee 11 D-89081 Ulm ------------------------ ============================================================== # This is a command file to be opened from UCSF Chimera. # It loads several molecules from PDB files, and arranges them in docked conformations. # These conformations are the result of a Bayesian inference carried out by FastNPS. # Upon execution of this file, Chimera will generate a movie clip showing a set of docked # conformations, in the manner of a flip-book. # This file can be edited if any particular colour or lighting options etc. are desired. # --- load PDBs --- open ./2waq.pdb open ./1D3U_movedtoCentrePol_noTFB.pdb ################################################################################## ##### E d i t a b l e s e c t i o n for custom viewing preferences ##### ##### (colour, lighting, background, etc.) ##### ################################################################################## set bg_color white color dark slate gray #0:.A-Q 2dlabel create title text "Samples of configurations of docking scenario, 2WAQ vs. 1D3U" xpos 0.04 ypos 0.92 color black 2dlabel create sub text "Motion does not represent dynamics" size 12 xpos 0.04 ypos 0.88 color black ################################################################################## ##### E n d o f e d i t a b l e s e c t i o n ##### ################################################################################## move x 14.5577 model #1 move y 10.7525 model #1 move z 13.1320 model #1 windowsize 800 600 scale 0.8 movie record supersample 3 move 0.9432,3.3367,-3.9733 model #1 wait move -3.1264,-2.5812,5.6072 model #1 wait move -2.9523,2.8959,-3.9907 model #1 wait move -14.0968,0.5720,-12.9560 model #1 perframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframeperframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe wait move 8.4475,0.1,0.1 model #1 perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe wait move 8.4475,4.5142,16.4771 model #1 turn z 2 wait move -12.9187,-0.7126,-7.8443 model #1 turn z 2 wait move 9.5982,-3.2342,8.4843 model #1 turn z 2 wait move 3.2604,3.3466,-4.2558 model #1 turn z 2 wait move 0.5383,-1.8787,5.0346 model #1 turn z 2 wait move -0.6887,1.1472,-2.6070 model #1 turn z 2 wait move -0.0759,-1.7268,1.1365 model #1 turn z 2 wait move -3.1444,0.7922,-1.0015 model #1 turn z 2 wait move 5.2841,0.0361,0.6118 model #1 turn z 2 wait movie encode docking.mp4 bitrate 10000 framerate 60

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multi protein complexes
by A G Szabo 09 Dec '15

09 Dec '15

I am working with a protein PDB 4KHZ. It is a recent PDB deposition of the maltose transporter system. It is a multisubunit protein complex. There are five separate chains that come together. I know how to select and visualize each of them or in pairs or whatever. Two of the subunits have a maltose substrate bound within their interior. I know how to visualize the maltose molecules using the Select menu. When I go to the Select menu, open Residues - click on GLC (Glucose) all of the maltose molecules become visible in both proteins. Is it possible somehow to visualize only one of the maltose molecules in one of the proteins in this case the maltose in chain E. - and not have the maltose in G or F visualized. Thank you Arthur G. Szabo Professor Emeritus Chemistry and Biochemistry. Wilfrid Laurier University.

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Re: [Chimera-users] Save the map after hide dust
by Tom Goddard 08 Dec '15

08 Dec '15

Hi Gary, Good to hear from you. The hide dust feature does not change the density map, it only hides the small connected surface pieces. You could set the map grid points to zero inside the dust blobs with the mask command. But first you need to be able to show only the dust and there is no command to do that. I've attached a Python script that does that. You select the map surface (ctrl-click) that you have done hide dust on, then open the surfinvert.py script to show only the dust. Then use the mask command mask #0 sel invert true to mask the density map (#0) to the selected surface (dust blobs only shown) and invert, since you want to keep everything outside the dust blobs, not everything inside the dust blobs. I tried it, works. But if you lower the threshold on the new map then of course you see more dust. Tom The surfinvert.py script is also on the Chimera Python scripts page http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > On Dec 8, 2015, at 5:05 PM, Gang (Gary) Ren wrote: > > Hi Tom, > > I like the density map after hide density map, is there any way to save the > density map after dust hide? Every time I save the density map, it saved the > original map instead of density map after hidden dust. > > Thanks a lot > Gary > > > >

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subregion selection of a map
by Anindito Sen 08 Dec '15

08 Dec '15

Dear All, Is there a simple way that I can select a portion of a map using 'subregion selection' option where I can change the orientation of box (used for selection). Thanks Andy

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Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan
by Engelhardt, Peter 08 Dec '15

08 Dec '15

Hi, No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... " (see attachment). This problem has not appeared in with earlier OSX updates! We hope this problem will be fixed soon. Cheers Peter Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt(a)Helsinki.Fi Email: Peter.Engelhardt(a)Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Monday, November 30, 2015 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 151, Issue 35 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. inserting missing residue (Francesco Pietra) ---------------------------------------------------------------------- Message: 1 Date: Mon, 30 Nov 2015 19:40:50 +0100 From: Francesco Pietra <chiendarret(a)gmail.com> To: chimera <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] inserting missing residue Message-ID: <CAEv0nmtYfsQJBkbzkypX+uzqbYU7EMLhFZrybVhzj5W1hdM_OQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi: II would like to insert a single non-terminal missing amino acid in a big peptide. By using MODELLER with CHIMERA, I don't find any option for NOT modeling loops. Just inserting the missing residue without moving the adjacent residues. In the sequence that appears by invoking modeling, the missing residue is not marked in any way, the sequence just continues as if no non-terminal residue were missing. thanks francesco pietra

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Copy the Rotation matrix and translation to the third image
by Morris, Kyle 08 Dec '15

08 Dec '15

Peggy, Tom graciously answers enough of my requests, so I can take some of the slack from him here, I asked this recently (Re: [Chimera-users] Volume transformation based on Phenix symmetry operators). You can use the ‘matrixset command. Save your 4x3 matrix to a text file with a header ‘Model 2.0’ then in chimera use the following: setmatrix /path/to/matrix/text/file This will translate and rotate model #2 according to the matrix in the file you saved from the reply log. This function is documented here http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/matrixset.html. Have fun! Best, Kyle Date: Tue, 8 Dec 2015 16:48:56 +0800 From: ??? <peggyschsu(a)gate.sinica.edu.tw<mailto:peggyschsu@gate.sinica.edu.tw>> To: <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] Copy the Rotation matrix and translation to the third image Message-ID: <009701d13195$45ce4850$d16ad8f0$(a)gate.sinica.edu.tw<mailto:009701d13195$45ce4850$d16ad8f0$@gate.sinica.edu.tw>> Content-Type: text/plain; charset="big5" Dear All, Here I had fitted two images with the function ?Fit in Map? and gotten the rotation matrix and translation value from the reply log. Could anyone help me to apply the same matrix and rotation to the third image? Thank you for your help! Sincerely, Peggy -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151208/7d37…> -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: application/octet-stream Size: 41241 bytes Desc: not available URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151208/7d37…> ------------------------------

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Cubic vop zone boxes
by Morris, Kyle 08 Dec '15

08 Dec '15

Hi Chimera team and users, I am cutting out multiple sub-volumes from a much larger volume (#0) with fitted PDB co-ordinates (#1-n) using a script, but having trouble making the final sub-volumes cubic. At present I am using cutting out sub-volumes using '$ vop zone #0 #1 10 minimalBounds true’ to make the sub-volume more manageable. I am aware of the previous questions posted at http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-April/010942.html for reducing a volume size and the trick at http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-April/006208.html for expanding a volume. Is there however a way to make the volume cubic at the vop zone stage or a one liner command to expand a box after cutting with minimalBounds so that this can be efficiently scripted? Thanks for your help! Kyle

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Copy the Rotation matrix and translation to the third image
by 許紹君 08 Dec '15

08 Dec '15

Dear All, Here I had fitted two images with the function “Fit in Map” and gotten the rotation matrix and translation value from the reply log. Could anyone help me to apply the same matrix and rotation to the third image? Thank you for your help! Sincerely, Peggy

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Edge lengths of virus particles
by vamsee 07 Dec '15

07 Dec '15

Hello Elaine, I am trying to find the edge lengths of virus particles using Chimera. The method I came up with is to 1. Create an icosahedron with the diameter of the virus. 2. Create two atoms that sit on adjacent vertices of the icosahedron 3. Measure the distance between the two atoms But this method gives me the edge length of the icosahedron and not the virus itself. Is it possible to get the edge lengths of the actual virus without having to go through this process? Thank you Vamsee

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Surface-display option
by Puthiyaveetil, Sujith 07 Dec '15

07 Dec '15

Hi Chimera developer, I encounter a problem with surface calculation/display when using the biological assembly (dimer) of 1Q90. The monomer on its own, as in pdb file 1Q90, displays the surface with no problem. I have tried the "split" command without success on the biological assembly. Also tried changing parameters to no effect. Would you please help. Regards, Sujith Sujith Puthiyaveetil Postdoctoral research associate Institute of Biological Chemistry Washington State University Pullman, WA 99164. Phone: +1 509-715-7435

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Re: [Chimera-users] helices
by Elaine Meng 07 Dec '15

07 Dec '15

Hi Arthur, There isn’t anything in the menu to do that, but it can be done with commands or in the Selection Inspector. I’ll describe one way. When you show ball-and-stick, the balls are at some fraction of the VDW radii. When you show spheres, it is the full VDW radii. You could change the VDW radii, but probably a better method is to show ball-and-stick but change what fraction they are of the VDW radii. The default is 0.25. To change it you could use a command something like: setattr m ballScale 0.5 That would make ball-and-stick balls half the radius of the spheres. Of course, you could try other values and just see what you like. The “m” is because this setting is for the whole molecule model; you can’t have different values for different atoms in the same model. You can show the command line from the Favorites menu. You can also make sticks fatter and thinner in a similar way, with stickScale (default 1.0). 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 On Nov 18, 2015, at 2:25 PM, A G Szabo <agszabo(a)bell.net> wrote: > Elaine > > But now I have another question that is related to the one I managed to > figure out. > > When I highlight an amino acid residue on a structure I know how to > visualize the amino acid as a ball and stick structure. I also know how to > have the residue shown as spheres. Except the Spheres are way too large. > > Is there a way in which I can reduce the size of the spheres? > > I couldn't find anything obvious in the Tools menu. > > Thank you > > Arthur G. Szabo

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(hopefully) simple rendering question
by Lybrand, Terry P. 03 Dec '15

03 Dec '15

Hello, I am looking for suggestions from the CHIMERA developers and users’ community to address a rendering problem I have. I have computed electric field data for protein ligand binding sites (wt and related mutants) and would like to render this field data as a collection of vectors, superimposed over a nice rendering of the binding site structures. The field results are from a series of QM/MM calculations we have performed, and are in a simple ASCII format: cartesian coordinates for N grid points, followed by cartesian coordinates of the N field vectors that originate from the corresponding grid points. I’ve debated whether I might be able to subvert the PseudoBond reader to somehow process these data, but still don’t have an easy option to display each field vector as a short arrow. Note that I don’t want to render the electric field data as a set of continuous color-coded field lines. That is easy in any number of molecular graphics programs. I know that rendering fields as a collection of vectors (arrows) is “old-fashioned”, but in this case we are convinced the old-fashioned render is a more effective way to communicate our results. Thanks in advance for any suggestions. Terry L. P.S. Greetings to all my former colleagues at UCSF. ++++++++++++++++++++++++++++++++++++++++++++ Terry P. Lybrand Prof. of Chemistry - College of Arts & Science Professor of Pharmacology - School of Medicine Vanderbilt University Center for Structural Biology 5-154C BioSciences/MRB III Nashville, TN 37232-8725 Telephone: 615-343-1247 Fax: 615-936-2211 e-mail: terry.p.lybrand(a)vanderbilt.edu<mailto:terry.p.lybrand@vanderbilt.edu> WWW: http://structbio.vanderbilt.edu/lybrand

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color actions on toolbar
by Julian von der Ecken 02 Dec '15

02 Dec '15

Hi, I use Chimera extensively and really appreciate its functionality! I work with "Color Actions” all the time and it would be so great to have it on the toolbar and not only the “Color Editor”. If you could incorporate it to the next release or let me know how to set it (I do not see it in "Favorites-Add to Favorites/Toolbar”)? Thanks in advanced Julian ————————————————————————————————— Julian von der Ecken Max-Planck-Institute of Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund, Germany room: B2.27 tel: (+49) (0)231 133-2307 e-mail: julian.von-der-ecken(a)mpi-dortmund.mpg.de lab: http://www.raunser-lab.de institute: http://www.mpi-dortmund.mpg.de

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Write a PDB with Python API
by Jaime Rodríguez-Guerra Pedregal 02 Dec '15

02 Dec '15

Hi again! So in my quest to use OpenMM from Chimera, my first proof-of-concept attempts consist of using a PDB file as intermediate to convert chimera.Molecule objects to OpenMM Topologies (using openmm.app.PDBFile loader). While not ideal yet, it'd be convenient to use StringIO() as a memory file, and I have been more or less successful. This is my strategy: memfile = StringIO() m = chimera.openModels.list() chimera.pdbWrite(m, m[0].openState.xform, memfile) memfile.seek(0) # pass memfile to openmm.app.PDBFile and do OpenMM stuff memfile.close() It works, but some residues are not properly recognised... I dumped the converted PDB to an actual file and saw that the problematic residue (an ARG) is totally messed up! I've attached the results: original file is the mol2, the converted one is the pdb, and also a Chimera session with both superimposed. What's the recommended method to convert a chimera.Molecule to a PDB file (if possible, in-memory) with Chimera Python API? Thanks a lot!

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Matchmaker 'restrict to selection' not working as expected.
by Oliver Clarke 01 Dec '15

01 Dec '15

Hi all, When using Matchmaker, the ‘Further restrict to matching selection’ option does not seem to improve the speed of alignment as much as expected under certain circumstances (when the selection is a subset of a larger chain, as opposed to being an individual chain in a multi chain structure). It seems to still restrict the selection correctly for the final alignment (it is still only aligned on the selected domain), but the “test match” step seems to be conducted on the entire chain, rather than the selection - this makes a big difference to speed for large proteins. For example - I tried aligning two conformations of a protein complex consisting of one chain A ~100 residues, and chain B ~5000 residues. If I select chain A of both structures, and then select ‘Further restrict to matching selection’ for both the reference and the structure to match, the alignment is almost instantaneous - less than 2s. If I perform the same operation, but this time selecting the first 100 residues of chain B in each structure, the alignment takes 3min20s, regardless of whether I leave automatic chain pairing on or select the specific chains to use for alignment manually. It takes only marginally longer - 5 min - if I select the entirety of chain B, a selection that is 50X the size. Incidentally I still get the “test match” message in the status bar even when the selection only contains one chain from each structure, or when I manually select (using the chain pairing options) which chains to align - maybe Chimera is still running test match on the whole chain when it should only do so on the selection (or not at all if the selection only includes one possible match). This seems like a bug? Or am I missing something? Cheers, Oliver.

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domain angel
by Smith Liu 01 Dec '15

01 Dec '15

Dear All, Is any way to calculate the angel between 2 domains by Chimera? Smith

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Installing OpenMM in Chimera
by Jaime Rodríguez-Guerra Pedregal 01 Dec '15

01 Dec '15

Hello, I am trying to install OpenMM in Chimera to script some molecular dynamics. However, I am struggling to make it work, since the build fails with this error: g++ -pthread -fPIC -mtune=generic -m64 -I/home/chimera/chimeraBuild_X11/build/build/include -L/home/chimera/chimeraBuild_X11/build/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -shared -Wl,--hash-style=both build/temp.linux-x86_64-2.7/src/swig_doxygen/OpenMMSwig.o -L/lib -R/lib -lOpenMM -lOpenMMAmoeba -lOpenMMRPMD -lOpenMMDrude -o build/lib.linux-x86_64-2.7/simtk/openmm/_openmm.so g++: error: unrecognized command line option '-R' which is probably not related to Chimera at all. What I've done so far: 1. Download precompiled binaries for Linux from their site: https://simtk.org/project/xml/downloads.xml?group_id=161 2. Extract that file and merge the contents of the directories "include" and "lib" with those in Chimera root path. 3. Cd into the python directory of the extracted file and run: chimera --nogui --script "setup.py install". Has somebody been successful with this package? I know it seems more of a compiler issue, but maybe Chimera is doing some trickery with the build mechanism too. Thank you in advance, Jaime.

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inserting missing residue
by Francesco Pietra 30 Nov '15

30 Nov '15

Hi: II would like to insert a single non-terminal missing amino acid in a big peptide. By using MODELLER with CHIMERA, I don't find any option for NOT modeling loops. Just inserting the missing residue without moving the adjacent residues. In the sequence that appears by invoking modeling, the missing residue is not marked in any way, the sequence just continues as if no non-terminal residue were missing. thanks francesco pietra

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Re: [Chimera-users] calculating dipole moment of a protein in pdb
by Eric Pettersen 25 Nov '15

25 Nov '15

Hi Ajay, Okay I have attached a script that also shows the dipole vector as an arrow on the structure. It will also be listed in the model panel so you can easily hide it or change its color. If you want it to be a different length, change the setting of the “vectorScale” variable in the script itself. The updated script is also available via the scripts page. —Eric > On Nov 25, 2015, at 12:11 PM, Pande, Ajay K <apande(a)albany.edu> wrote: > > I really do need it for many structures, and I am reasonable certain many other people will too. What would be nice is that the dipole vector shows as an arrow on the pdb structure. If you can change the script file, it would be very useful. > > Thanks > > Ajay > > > > > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Sent: Wednesday, November 25, 2015 2:50 PM > To: Pande, Ajay K > Cc: chimera List > Subject: Re: [Chimera-users] calculating dipole moment of a protein in pdb > > >> On Nov 23, 2015, at 10:37 AM, Pande, Ajay K <apande(a)albany.edu <mailto:apande@albany.edu>> wrote: >> >> Hi Eric, >> >> It does give me the numerical value of the dipole moment, but how do I generate the dipole vector in the pdb structure? >> >> Thanks >> >> Ajay > > If you add the following two lines to the script it will print out the center of mass and dipole vector: > > print “center of mass:”, com.data() > print “dipole:”, dipole.data() > > Make sure the lines are indented to the same level as the final print statement in the original script. With those values you can easily write a BILD format file that will draw an arrow from the center of mass to the (center of mass + dipole) and open that file to show the arrow. The BILD format is described here: > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/bild.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/bild.html> > > If you are doing this for many structures, it would be possible to modify the script itself to create/open the BILD file, but that would be significantly more work. But if you really need it let me know. > > —Eric > >> >> >> >> >> >> >> From: Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> >> Sent: Thursday, November 19, 2015 7:56 PM >> To: Pande, Ajay K >> Cc: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Subject: Re: [Chimera-users] calculating dipole moment of a protein in pdb >> >> Hi Ajay, >> The script referenced in this chimera-users archive message will compute it: >> >> http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html> >> [Chimera-users] BCC CHARGES >> I've attached a script that if you run it (File->Open, or "open ~/ dipole.py" [if it's in your home directory]) will print the dipole moments of all open molecular ... >> Read more... <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html> >> >> Extracting the script from that message may be challenging, so I’m attaching it again. It’s also available from our Chimera Scripts page: >> >> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> >> >> Like it says in the original message you have to assign partial charges before running the script (Tools->Structure Editing->AddCharge, or the “addcharge” command). >> >> —Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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calculating dipole moment of a protein in pdb
by Pande, Ajay K 25 Nov '15

25 Nov '15

Could you please tell me how to calculate the dipole moment of a protein in Chimera, given its pdb file? Thanks Ajay

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on ligand
by Smith Liu 25 Nov '15

25 Nov '15

Dear All, When we display a protein-ligand complex by chimera, the sidechains of residues around the ligand will be displayed. Will you please tell me by which criteria chimera select the residues arond the ligand for display? And how to change this criteria in the command input format? SMith

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feature request - add "save relative to model" as optional default?
by Oliver Clarke 25 Nov '15

25 Nov '15

Hi, Nitpick-y request for a future version but one that would make life easier... in the “Save PDB" dialog, would it be possible (when the option is present) to default (perhaps optionally) to having the “Save relative to model” box checked (and have the selected model default to the starting model)? I often save a manipulated pdb, or one that has been rigid-body fit to a density map, then open it up in coot or another program and realize that the map and model are no longer aligned because I forgot to check this box, and I can’t think of many cases when I would deliberately uncheck it. Cheers, Oliver.

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Re: [Chimera-users] scale problem
by Yaowang Li 24 Nov '15

24 Nov '15

Dear all, I faced a scale problem when I was trying to fit the density map. A density map was reconstructed from a set of projections which their magnitude are 1.055A/pixel, with a reference model that is 1.055 A/voxel and 5 A in resolution. However the pdb file cannot fit into the map because the map is too much small. So I have to change the voxel size to double and then can be fitted. Here I changed the voxel size, I think it changed the scale for the density. So i just worried about the fitting result. thanks On Sun, Nov 22, 2015 at 10:07 AM, Yaowang Li <liyaowang2911(a)gmail.com> wrote: > Dear all, > > > I faced a scale problem when I was trying to fit the density map. > > A density map was reconstructed from a set of projections which their > magnitude are 1.055A/pixel, with a reference model that is 1.055 A/voxel > and 5 A in resolution. However the pdb file cannot fit into the map > because the map is too much small. So I have to change the voxel size to > double and then can be fitted. > > Here I changed the voxel size, I think it changed the scale for the > density. So i just worried about the fitting result. > > thanks > > yaowang > > > > >

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