- Chimera-users - RBVI Mailing Lists

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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Re: [Chimera-users] Calculation of the average isoelectric point of a proteins solvation shell
by Elaine Meng 23 Nov '15

23 Nov '15

> On Nov 21, 2015, at 11:54 AM, Csaba Nagy <csaba.nagy(a)utu.fi> wrote: > > Dear Elaine, > > thank you for your kind reply, and for the instructions regarding the surface charge of the protein. I just realized, that I phrased my question wrong, actually I wanted to calculate the average isoelectric constant of the proteins surface-amino acids in order to apply the most optimal buffer system to solubilize my protein. > Thank you again. > > Best wishes, > Csaba > Dear Csaba, Sorry, Chimera does not calculate isoelectric points or constants, it only estimates charge in aqueous solution near neutral pH. You would need to find some other program to do what you want. It is best to send Chimera questions to the chimera-users(a)cgl.ucsf.edu list, CC’d here. Apologies if you got this message more than once, I was having trouble sending the e-mail. 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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How to insert a morph into a movie command file?
by Christina Bourne 23 Nov '15

23 Nov '15

Dear all, Is there a straightforward way to insert a morph within a larger movie? We are working from command scripts but see that the command "morph" is not recognized.Any help is appreciated,Christina

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Dock prep with multiple structures - endless loop?
by Oliver Clarke 20 Nov '15

20 Nov '15

Hi, Would it be possible to add a progress bar (with ETA) for Dock prep at some point? I ran it overnight to fill partial sidechains on six structures (each ~6000aas), and it still isn’t finished, but I can’t tell whether it is just taking a really long time or whether something has gone wrong. The status bar is still updating with “Matching donors”, “finding acceptors” and “building search tree” messages, but it seems to be giving these messages multiple times for each structure - is that normal? Cheers, Oliver.

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Inter-molecular H-bonds between water molecules not displayed in per-frame script
by George Green 20 Nov '15

20 Nov '15

Hi, I'm trying to get a per-frame script going which shows the inter-molecular H-bonds within a protein binding site. It is working in that all H-bonds show apart from water-water h-bonds. Is there any fix for this at all? My code is below: Water molecules are residues :159-162 I would be very grateful for any assistance. :) sg ################################################ #################### # per-frame H-bond repr bs :158 color hot pink :158 color byhet :158 # disp :60,37,85,112,109,35,158,84,60,40,38,114,69,90,58,61-68,56,21,45,52,101,15,92,40,105,116,24,42,54,40,24,10,97,120,159,160,161,162 disp :WAT # select :1-162; hbonds intramodel true intermodel true line 5 color gold ; ~select select :90 ################################################

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Calculation of the average isoelectric point of a proteins solvation shell
by Csaba Nagy 20 Nov '15

20 Nov '15

Dear Chimera Developers and -Users, I am struggling with the overexpression and purification of a cytoplasmic protein that looks to be soluble only in a very narrow pH range. I know the average isoelectric point of the whole protein, but there would be much more informative, to know what is the average isoelectric point of the proteins solvation shell, I think. Therefore I modeled the 3D structure of the protein and I tried several other visualization programs to calculate this pI value, but I was not successful. Could you tell me please, if there is any option to make this estimation in Chimera? Thank you very much in advance! Best regards, Csaba Nagy ------------------------------- Csaba I. Nagy, PhD Postdoctoral Researcher, PharmaCity, Itäinen Pitkäkatu 4 C, 6th floor, room 6049 Molecular Plant Biology University of Turku FI-20014 TURKU, Finland Phone +358 2 333 7914 Fax +358 2 333 8075 Email csaba.nagy(a)utu.fi --------------------------------

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command line issues
by liz kellogg 19 Nov '15

19 Nov '15

Hi, I've been using chimera quite happily for the past couple of years. I especially like the command line, as it makes operations much faster to complete (once you know the commands!) I've been using the command-line, in chimera, on my mac (osx yosemite version 10.10.3) for a while now, but just today my command-line would not display the text I'm entering into the command-line bar. This is odd, I've never seen this before, and I don't know what the problem is due to. I tried restarting chimera, I tried restarting my computer, and I tried re-installing chimera, but the command-line prompt is the same.. it doesn't display the text as I'm entering it.. though if I type a command, it does execute it and it shows up in the command history.. so it looks like a problem in displaying text as it's being entered. Has anyone else run into this problem? And how do you fix it? I'd be so much happier if I could see what I'm typing! thanks Liz

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Uploading to Microsoft Word
by Austin Brown 19 Nov '15

19 Nov '15

Hello, I am working on a project that involves uploading 10-15 Chimera images to a Microsoft Word document. The first time I got all of them on there, they looked great. However, upon opening my project the next morning, all the images were blank with a small red X in the corner. There was an error message that read "The image part with relationship ID rld5 was not found in the file." I am not sure what went wrong, but it's just a .png picture that I saved through Chimera. I am running on a Mac with Microsoft Word 2013. Any help is appreciated. Thanks, Austin

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Calculation of the average isoelectric point of a proteins solvation shell
by Csaba Nagy 19 Nov '15

19 Nov '15

Dear Chimera Developers, I am struggling with the overexpression and purification of a cytoplasmic protein that looks to be soluble only in a very narrow pH range. I know the average isoelectric point of the whole protein, but there would be much more informative, to know what is the average isoelectric point of the proteins solvation shell, I think. Therefore I modeled the 3D structure of the protein and I tried several other visualization programs to calculate this pI value, but I was not successful. Could you tell me please, if there is any option to make this estimation in Chimera? Thank you very much in advance! Best regards, Csaba Nagy ------------------------------- Csaba I. Nagy, PhD Postdoctoral Researcher, PharmaCity, Itäinen Pitkäkatu 4 C, 6th floor, room 6049 Molecular Plant Biology University of Turku FI-20014 TURKU, Finland Phone +358 2 333 7914 Fax +358 2 333 8075 Email csaba.nagy(a)utu.fi --------------------------------

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Re: [Chimera-users] RMSD script
by Elaine Meng 18 Nov '15

18 Nov '15

Yes, as described in more detail in the “RMSD Analysis” description you can select specific atoms (for example command “select protein & @n,ca,c,o” to select the peptide backbone atoms) and use the “Restrict map to current selection, if any” option. That option is on by default. If it was on and you didn’t select any atoms, it used all atoms. > See MD Movie manpage, especially sections “Startup and Input” and “RMSD Analysis" > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> More about selection: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> Best, Elaine On Nov 18, 2015, at 2:47 PM, Ruth Nelson <Ruth.Nelson.180(a)nd.edu> wrote: > Hi Elaine, thank you for your response. > > Using MD Movie worked to calculated the RMSDs, but I am unsure if the output values are full atom or for the backbone (Ca, C, N, O) only. Is there some way I can specify this? > > Thank you very much, > Ruthie > > On Wed, Nov 18, 2015 at 5:06 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Ruthie, > If all of the PDB files have exactly the same atoms with the same names, and no END lines, you could try opening all of them as one trajectory in MD Movie. That tool has an all-by-all RMSD calculation option and you can save the results to a text file. You would still have to process that file into CSV, however, as there is no CSV output option, but this would greatly decress the number of steps you have to script yourself, and it would be done outside of Chimera in whatever type of scripting you prefer. > > I.e. you would start MD Movie ( in menu under Tools… MD/Ensemble Analysis) and then choose to open the trajectory as PDB, multiple files. They have be named similarly with numbers but the numbers don’t have to be consecutive. If loading the trajectory is successful, the MD Movie playback dialog will appear, and from that dialog you could choose Analysis…RMSD Map. The RMSD can be calculated from all atoms or only specify ones that you have selected. Then there is a button to “Save RMSDs” on the resulting map window. > > See MD Movie manpage, especially sections “Startup and Input” and “RMSD Analysis" > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> > > 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 9:38 AM, Ruth Nelson <Ruth.Nelson.180(a)nd.edu> wrote: > > > Hello, > > > > I have a matrix of 10x10 .pdb files, and I need to calculate the RMSD from each PDB file to every other PDB file in that matrix. When I do this in the command line of Chimera, I type something like "match #0 #1" or "match #0 #2" for each of my PDB files, but I would like to automate this process so that it does not take as long. I have hundreds of files and they are all are named similarly (file_1.pdb, for example) but they are not numbered consecutively (file_1.pdb, file_17.pdb, file_43.pdb, for example). If possible, I would like the RMSD values to be output into a CSV file so that I can open it in excel. > > > > I have very little experience writing scripts and no idea where to begin to write this one, so I would greatly appreciate any help. I have been reading some of the responses given to other people regarding similar scripts, but I am having a hard time translating that to what I would like to do. > > > > Thank you very much, > > Ruthie > > > > > > > -- > Ruth Nelson, Graduate Student > Department of Chemistry and Biochemistry > University of Notre Dame > rnelson9(a)nd.edu

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RMSD script
by Ruth Nelson 18 Nov '15

18 Nov '15

Hello, I have a matrix of 10x10 .pdb files, and I need to calculate the RMSD from each PDB file to every other PDB file in that matrix. When I do this in the command line of Chimera, I type something like "match #0 #1" or "match #0 #2" for each of my PDB files, but I would like to automate this process so that it does not take as long. I have hundreds of files and they are all are named similarly (file_1.pdb, for example) but they are not numbered consecutively (file_1.pdb, file_17.pdb, file_43.pdb, for example). If possible, I would like the RMSD values to be output into a CSV file so that I can open it in excel. I have very little experience writing scripts and no idea where to begin to write this one, so I would greatly appreciate any help. I have been reading some of the responses given to other people regarding similar scripts, but I am having a hard time translating that to what I would like to do. Thank you very much, Ruthie

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Changing default framerate of Animation tool
by Eiros Zamora, Juan 17 Nov '15

17 Nov '15

Dear Chimera experts, I would like to know if there’s a way to increase the default 25 fps framerate when using the ‘Animation' tool to make movies. I tried increasing it from the ‘Movie Recorder’ menu, but it’s still producing the video at 25 fps. Also, I am not sure about what does the ‘Nth frame for discrete transitions’ property of items in the timeline mean. Should I increase this to get more FPS? I would like to do this because I am trying to do a video of an MD trajectory showing at the beginning the water box (and then hiding it), but at the moment the videos that I am getting feel very ‘clunky’ Cheers Juan

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how to prepare ligand by command line?
by Albert 17 Nov '15

17 Nov '15

Hello: I've got a ligand in 2D .sdf format without any hydrogens. I am just wondering how can we prepare this compound for docking? Is it possible to run it by command from Chimera? Thanks a lot Albert

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Problem using Chimera
by BRUXELLES Tatiana (ETU VIE) 17 Nov '15

17 Nov '15

Dear Sir, dear Madam I am a Master student at the Université de Strasbourg in France and I am currently doing an internship in a bioinformatics lab : the LBGI in Strasbourg. One of my tasks during this internship is to make Chimera read about 80 files with the extensions .scf. The problem is that software doesn't to be able to read my command file. I can't even make it read a print instruction. To execute those files I use the command : read File_name in command line on chimera. I am gonna join the files so you can see. Could you suggest a solution to my problem ? Kind regards, Bruxelles Tatiana

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helices
by A G Szabo 17 Nov '15

17 Nov '15

I sent a message yesterday regarding how I can change helices from ribbons to smooth wires. I am pleased that I can indicate that I figured it out.. Arthur G Szabo Professor Emeritus Wilfrid Laurier University

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smooth backbones
by A G Szabo 16 Nov '15

16 Nov '15

I have no problems with ribbons. However I would like to show some helices as backbones only. How can I achieve the result shown on the attachment for this helix. Don't know where to start looking. Any " Actions" only gave me this. Thank you Arthur G. Szabo Professor Emeritus Wilfrid Laurier University

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isosurface and blobs
by Raffaele Raucci 12 Nov '15

12 Nov '15

Hi all, I imported in chimera a map file with .cube extension. I was able to show isosurface after setting specific isovalue. Can you tell me if it is possible, by command line, count the number of different blobs displayed as isosurface? Is it also possible determine the area and volume of each blob? Thanks in advance, Raphael

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Volume transformation based on Phenix symmetry operators
by Morris, Kyle 12 Nov '15

12 Nov '15

Dear Chimera developers and community, I have a volume and an associated symmetry operator identified by another software package for this map. I would like to transform the map according to the symmetry operator to inspect what the symmetry related map looks like, does anyone know how to do this based on the appended matrix? Thanks in advance for your help! Best wishes, Kyle ================================== >From Phenix: new_operator rota_matrix -0.0877 -0.5114 0.8549 rota_matrix 0.9251 -0.3601 -0.1206 rota_matrix 0.3695 0.7803 0.5047 tran_orth 578.6845 434.1862 -508.9168 center_orth 918.6495 790.3525 1034.0200

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ESP
by Putkey, John 12 Nov '15

12 Nov '15

I have a question about electrostatic surface potential coloring. It works fine when only one .pqr and .dx file is open. I can uncolor, recolor and adjust the ESP color scale, but odd things happen when muliple .pqr and .dx files are open. Strange color patterns are obtained even though the correct MSMS surface and .dx file are selected in the Surface Color dialog box. Its as if the program is reading two .dx files. Is it me or a bug with the system? Cheers John John A. Putkey Professor Biochemistry and Molecular Biology University of Texas Medical School 6431 Fannin Houston Texas, 77030 John.Putkey(a)uth.tmc.edu<mailto:John.Putkey@uth.tmc.edu> (713) 500-6061 Office (713) 500-6062 Laboratory (713) 500-5073 NMR Laboratory

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Chimera 2 release date
by Markus Heller 12 Nov '15

12 Nov '15

Hello, Just curious, what's the anticipated release date for Chimera 2? Couldn't find it on the homepage ... Thanks Markus

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Built-in residue specific annotations in mmCIF?
by Oliver Clarke 12 Nov '15

12 Nov '15

Hi all, As discussed on the ccp4bb (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511>), the mmCIF format incorporates an atom_sites_foornote record (http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_site…) which allows for the direct association of specific comments/annotations with particular atoms/residues. As part of expanding mmCIF support in Chimera2, would it be possible to consider incorporating the capacity to read, write, and display these records as labels or notes? This could be a great way of incorporating built-in-annotations in a structure pertaining to specific features that could potentially be readable by other software such as Coot and pymol. Cheers, Oliver.

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Re: [Chimera-users] compounds
by Elaine Meng 09 Nov '15

09 Nov '15

Dear Dwey, You can use “Join Models” to join any structures that are open as two separate models (from two separate input files). You just couldn’t use the “peptide” option in that tool if they are not peptides; you would have to use the “other bond” option. See the Join Models part of the Build Structure tool for details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> You are more likely to find answers to questions in the User’s Guide than in the chimera-users archive. You can search the User’s Guide with menu: Help… Search Documentation. If that doesn’t help, then emailing the forum (CC’d here) is recommended unless you are including private data. 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 9, 2015, at 2:05 PM, MPI <mpi566(a)gmail.com> wrote: > > Dear Elaine > Thanks for kindly answering my questions in Chimera forum. > > I have a question related to compounds and I appreciate your > valuable oppions. > > Let's say I have compound A and compund B. Both have strucctures. > > I would like to use a moiety (part) of compound A and a moeity > (part) of compound B. I wonder if Chimera can combine the desired > moeities of compound A and compound B to generate a new compound C. > > Another simpler version. Can Cimera merge compound A and > compound B into compound D ? > > I checked Chimera list but I found that Chimera provides a > function of joining models NOT for "compounds/drugs" but rather for > "Proteins". I also see you made comments in the past. I wonder if > you can provide insights into "compounds" or some hints to allow me > working on compounds in Chimera. > Many thanks, > Dwey

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obj file origin
by Erin Cutts 08 Nov '15

08 Nov '15

I am trying to use the .obj file generated as a surface mesh. Where the chimera outputs it as a list of vertices (points in 3D), a list of nomals (which I ignore) and a list of faces defined by 3 vertex reference numbers, it is super easy to import this into any mesh handling software. The problem is it seems to reset the orgin (the 0,0,0 point) to some mysterious location. As I am trying to compare this to electrostatics stored in a grid mesh format, where the orgin is specified, it would be nice if I could find out where the .obj has translated the axis coordinates too... The problem could also be caused by Chimera loading the molecule with a translation. All this gets very hard to deal with and trace...Any ideas that doesn't lead to me getting lost in cartesian space?

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3D dashed pseudobond styles?
by Oliver Clarke 07 Nov '15

07 Nov '15

Hi all, Feature request - more 3D psuedobond styles (for missing segments and metal coordination) would be nice. Specifically, small spheres (3D equivalent of dotted line) and cylinders with either rounded or flat ends (3D equivalent of dashed lines) would be very helpful. Often when used in combination with 3X3 or 4X4 supersampling, pseudobonds drawn in wire representation become too thin to see, whereas this is not the case for bonds or other 3D elements of the structure. Normally this doesn’t matter, because I can just redraw these bonds in a vector graphics program, but for stereo figures this doesn’t work. There is already one such option (representing pseudo bonds as sticks), but this looks weird - dashing or dotting is I think desirable to avoid confusion with regular bonds. Also, is there any way to add a custom pseudo bond (not a distance, no label) between a single pair of selected atoms? Similar to the dist command? This would be very helpful, for example, when trying to highlight a handful of specific interactions of a ligand with active site residues. One more while I’m thinking of it - a bit out there and certainly not for chimera 1 - it would be great to have a way of arranging 3D labels for residues such that they are displaced from the structure (perhaps arranged in a circle on the x-y plane), but with lines or arrows connecting them back to the residues they are labeling - this would be particularly great for generating labeled stereo figures, which is otherwise hard to do. Cheers, Oliver.

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resmap
by R.I.Koning＠lumc.nl 05 Nov '15

05 Nov '15

I want to use the colors representing resolution in Resmap to color the surface of my map. From what I understand from the documentation the script that automatically runs after Resmap is finished and “… color the surface of your input map with the results of ResMap…”. This last thing does not happen. Though this script seems to run (I see a slice depicting the remap (in 2D) moving back and forth in chimera somehow only a map with 1 slice opens in Chimera afterwards and I cannot use the resolution color coding for my surface. Should some sort of 3D file be generated that can be used to do this via Surface color or should the coloring be on the surface map by default? Both is not possible now. Best regards, Roman

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Using pip/easy install in Python 2.7.8 included in Chimera
by Ahir Pushpanath 05 Nov '15

05 Nov '15

Dear Chimera Team, As I specifically want to use the python included with chimera as the main python distribution available on my system, I am limited to using the python version shipped with it, as a standard. This is no problem for me, however, I am struggling to get pip /easy install working with the inbuilt python, namely because of errors between "urllib3" and python versions below 2.7.10. So, I keep getting HTTPS errors. Is there any way to use pip and easy install properly with the inbuilt Chimera Python? I did see a section called "import python modules into Chimera", but it appears as though that requires an additional python distribution to be present on the system? Please do let me know. Ahir If the reader of this email is not the intended recipient(s), please be advised that any dissemination, distribution or copying of this information is strictly prohibited. Johnson Matthey Plc has its main place of business at 5th Floor, 25 Farringdon Street, London (020 7269 8400). Johnson Matthey Public Limited Company Registered Office: 5th Floor, 25 Farringdon Street, London EC4A 4AB Registered in England No 33774 Whilst Johnson Matthey aims to keep its network free from viruses you should note that we are unable to scan certain emails, particularly if any part is encrypted or password-protected, and accordingly you are strongly advised to check this email and any attachments for viruses. The company shall not accept any liability with regard to computer viruses transferred by way of email. Please note that your communication may be monitored in accordance with Johnson Matthey internal policy documentation.

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Append PDB file to all individual PDB chains
by Carl Brown 04 Nov '15

04 Nov '15

To Whom This May Concern: In previous discussions, you explained how you could append two PDB files through the "join models" function: Discussion: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2011-April/006245.html> Build Structure: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht…> I would like attach a second PDB file to an initial one as well. However, my primary PDB file is a tetramer, made up of four identical chains. I would like to attach the second PDB to each of the four chains at the C-terminus. Is this possible? If so, how would I go about this? My concern is that using the "join models" function, it will only append the second PDB file once to the whole structure instead of to each individual chain. Cheers, Carl

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Open .pse file in Chimera?
by Desiree Benefield 04 Nov '15

04 Nov '15

Dear all, I have a .pse file generated with MacPyMOL that I would like to try to dock into a EM density map using Chimera. It would appear that this is not possible. Can you offer any advice or alternative approaches to try? With many thanks, Dez

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Silhouettes and depth cueing
by Oliver Clarke 02 Nov '15

02 Nov '15

Hi all, I’ve noticed that the intensity/color of silhouettes does not vary with depth cueing the way everything else does - normally this is fine, except when one is showing a slab of a structure - fragments of secondary structural elements which would otherwise blend into the background tend to become overly emphasized by the presence of silhouettes. The obvious solution to this for now is to turn off silhouettes when making these kinds of figures, but I quite like the effect that silhouettes provide, so I would rather not do so if there is an alternative. Perhaps in Chimera 2 it may be worth considering applying a depth dependent factor to the silhouette color (so it fades into the background color as it approaches the yon clipping plane)? Cheers, Oliver.

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Changes in transparency during animation
by Ashley Acevedo 02 Nov '15

02 Nov '15

Hi, I'm trying to animate a change in surface transparency. I have made a scene with my molecule at 0% transparency and a second scene with the same molecule at 70% transparency. The problem that I'm having is that when I set the transparency in one scene that transparency setting is carried over to my other scene, so I end up not being able to animate changes in transparency. Is there a solution to this problem? I'm using Chimera version 1.10.2 on a mac. Thanks, Ashley

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Non-alphanumeric character in keyword
by MPI 31 Oct '15

31 Oct '15

Dear users, In Chimera, I tried to run a vina docking in command line like vina docking receptor #0 ligand #1 output mytest search_center 10,20,30 There is an error: Non-alphanumeric character in keyword 'search_center' I have tried tweaking the keyword 'search_center' in different ways but the error won't go. Dose anyone know how to fix it ? or is this format correct ? Many thanks, Dwey

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Keep path when opening chimera from command line
by Eiros Zamora, Juan 30 Oct '15

30 Oct '15

Dear Chimera experts, I am working with Mac OS X version 10.11.1 and Chimera 1.10.2 I use Chimera to visualize MD trajectories. Usually I launch the program through the command line. I’ve got a pretty deep hierarchy of directories to keep my data organized, so I’ve been trying to look for a way to make Chimera keep the path of the directory where I launched it from, with no success. What I mean is, if I launch it from a given directory and then try to load MD NetCDF files with the “MD Movie” option, is there a way for it to show me the files in the directory where I opened it from?. Because now what it does is show me the ones from the last time I used this. Also, is there a way to load the topology and trajectories directly from the command line? I have looked for this option but haven’t found anything. Thanks for your help Juan

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Move molecule to center of rotation?
by Oliver Clarke 30 Oct '15

30 Oct '15

Hi all, Feature suggestion - it would be very useful if there was a way to automatically move a specific molecule to the current center of rotation (relative to all other models). I can do this manually by deactivating all other models for motion and moving using the “move” command or the mouse, but it seems like this could be made much quicker by automatically applying the translations necessary to bring a given molecule to the current center of rotation. I can probably do this using a python script but I think it is also a generally useful feature, particularly when fitting multiple protein components to a density map, or bringing in a ligand, etc. Cheers, Oliver.

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Molmap incorporation of B-factors
by Oliver Clarke 29 Oct '15

29 Oct '15

Hi all, For the purposes of model validation, I’d like to analyze local correlation of my model with the experimental map (and color it on either/both the model or map). I figured the easiest way to do this is to use molmap to generate a synthetic map, then use vop local correlation to generate a correlation map which I can use to color either the model or map (using scolor or “Values at Atom Positions”). This works fine, and generates informative looking pictures, I just wanted to clarify exactly what molmap is doing, to make sure I understand it. Am I correct in thinking molmap does not use a per-atom temperature factor (or alter the width of the gaussian depending on the atomic B-factor)? Because if this is the case I guess the way I am doing things will exaggerate how bad the model is in regions where the B-factor is high and the density weak (which is not the worst thing in the world - better than having an unrealistically rosy view of one’s model!). Would it be possible to incorporate atomic B-factors into molmap calculations for Chimera 2? Or does anyone know of an external program that will perform a similar calculation (I know I can generate RSCC plots in Phenix which must be doing this internally, but I rather like displaying it on the model and map for ease of interpretation). Cheers, Oliver.

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Keep electrostatic surface color without using map
by Tom Goddard 29 Oct '15

29 Oct '15

Hi Joshua, If you color a molecular surface with the Electrostatic Coloring tool in Chimera (menu Tools / Surface & Binding Analysis) using a Delphi or APBS electrostatics map, then close the map file using Model Panel (menu Favorites), then save the session (menu File / Save Session As…), then restart Chimera and load the session and the surface coloring is still there but the map is not used. Tested in current Chimera version 1.10.2. Tom > On Oct 28, 2015, at 8:22 PM, Broyde, Joshua E. wrote: > > Dear Tom, > Hope all is going well. I had a quick question about coloring surfaces by electrostatics and other properties. Currently, when you color surfaces with electrostatic potentials (e.g. with delphi .phi files) the molecular surfaces are colored by the delphi files, which are loaded into the chimera session everytime the chimera session is loaded. If the delphi files are deleted, the surfaces cannot be colored. Also, the delphi file has to be loaded every time the session is started, which can take a very long time (some of these delphi files are > 1 G). Is there a way to "permanently" color the molecular surfaces with the electrostatic potential, so that the delphi files have to be loaded only once? > > Sincerely, > Joshua Broyde

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movie related commands
by Smith Liu 27 Oct '15

27 Oct '15

Dear All, For the scale command, it will change (enlarge or decrease) the view immediately. Is any way we change the view gradually, for example in 10 frames or 100 frames? For the center command, it will also change the view immediately. Is any way we change the view gradually, for example in 10 frames or 100 frames? Best regards. Smith

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AM1-BCC: Question
by José Luis 26 Oct '15

26 Oct '15

Dears Devepolers: My name is José Luis. PhD student and to run docking and MD I was using Chimera 1.3 for AM1-BCC partial charges calculationwithour problem. Now, I´m using 1.10 and 1.10.2 but in the firt one the calculation doesn´t complete it and in the second one the following message appears: the system can´t find C:\Program Files\Chimera 1.10.2\share\chimeraInit.py", line 259, in CreateProcess current_directory, startup_info). Can you help me? Many thanks in advance. José Luis --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus

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Access to "Match Align" programmatically
by Miguel Ortiz Lombardía 26 Oct '15

26 Oct '15

Hi, Is it possible to call "Match Align" from a script or a 'com' file without using the GUI? I would use that possibility, if it does exist, to check pair-wise rmsd's of previously superimposed structures. I guess people may have asked this question before, but I couldn't find an answer in the usual places... Cheers, Miguel

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Query on Cryo-EM map
by Aditya Padhi 25 Oct '15

25 Oct '15

Dear Chimera Users, I have a cryo-em map file and I would like to convert it into a PDB file. How can I do that? I tried saving the .pdb file but it throws an error saying “No model chosen to save”. Another question, If I open a .map file of a protein complex in Chimera, how can I select a subregion (a particular chain) and colour the surface of that part differently? I am not able to select the chain when I upload the .map file. Thank you, Aditya

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How to make a microtubule model
by Tom Goddard 22 Oct '15

22 Oct '15

The following page shows a “bent microtubule” model made with a Chimera Python script https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html <https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html> The bend makes it more complicated than a straight microtubule. Here is an explanation of how the Chimera “sym” command can make a straight microtubule model. These commands in Chimera (menu Favorites / Command-line to enter commands) make a straight microtubule from a PDB model as shown in the attached image. open 1jff sym #0 group h,9.8,27.7,13*shift,8,80.0 surf true axis x center 0,115,0 res 5 The sym command took the tubulin dimer (shown in red and blue in the image) and made copies in a helical pattern to look like a microtuble. The trick is to find the right helical parameters. I just did a few minutes trial and error to find the above. The “group” option says make a helix where each subunit is shifted 9.8 Angstroms from the previous one and by 27.7 degrees around the axis from the previous one, and make 13 copies (for a 13 protofilament microtubule). This makes a single turn of the microtubule. A microtubule does not have helical symmetry, the one turn achieves a shift of 1.5 subunits creating a seam where alpha and beta tubulin are touching in two adjacent protofilaments. So I just make one turn. Then the above command says shift that one turn by 80 Angstroms along the axis for each of 8 copies. The “surf true” option says show the copies as surfaces. Without that it will copy the atomic model and use a ton of memory. The helix axis is x (just judged by eye after opening tubulin dimer 1jff. The 1jff dimer seems to be centered not far from 0,0,0 so I shifted the helix axis 115 Angstroms along y to make the diameter about 23 nm. Here are the docs for the sym command: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html> Here’s a web page where I did something more sensible to get better symmetry parameters — I fit the tubulin dimer to an EM map of a microtubule. http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html <http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html> Tom

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center of mass
by erik.laurini＠di3.units.it 21 Oct '15

21 Oct '15

Dear Chimera users, I would to plot the distance between the centers of mass of a ligand and a specific portion of its biologic target during the corresponding MD trajectory. I tried with the "MD plot" but it seems that it works only with atom selection. Do you have any advice? Thanks in advance! -erik- Dr. Erik Laurini Department of Engineering and Architecture University of Trieste, Via Valerio 10, 34127, Trieste (Italy) Tel. + 39 0405583440

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Calculating the total areaSAS from a series of PDB files
by ros 21 Oct '15

21 Oct '15

Hello! I would like to measure the SAS from a series of PDB files to see how the surface value changes over time (the PDB files are from an MD simulation). I know that If I open a PDB file and calculate the surface, I get the areaSAS value, but I do not want to do this 5000 times. I am making progress on a python script to automate the process, which is: -------------------------------------------- import os from chimera import runCommand as rc from chimera import replyobj os.chdir("/home/tmp/pdb") file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] for fn in file_names: replyobj.status("Processing " + fn) rc("open " + fn) rc("surf") rc("sel :1-6") from chimera.selection import currentResidues residues = currentResidues() outf = open("/home/tmp/sas.dat", "w") for r in residues: print>>outf, r, r.areaSAS rc("stop now") -------------------------------------------- The PDB's consist of only 6 residues (DNA residues). With this script, I get the output: #1 DA 1 320.8377808 #2 DC 3 277.614161432 #2 DG 4 323.883637217 #1 DC 3 284.934065707 #2 DT 6 221.04715555 #0 DA 1 321.883850728 #1 DC 5 345.231659889 #0 DC 2 179.379177183 #2 DC 5 350.455405176 #0 DC 3 285.785918236 #1 DT 6 245.048330456 #0 DG 4 303.501165912 #1 DG 4 314.409510799 #0 DC 5 352.639633257 #1 DC 2 193.509086639 #0 DT 6 214.883334659 #2 DC 2 183.766654447 #2 DA 1 344.369126737 using 3 test pdb's. Is there a way to get the total value of areaSAS of each model and not for each residue? I am interested in having a file just like (using for example 3 pdb's): Model # total areaSAS value #0 123123.123122 #1 123123.12312 #3 123123.12312 ... etc. I have tried deleting the residues loop, but I do not know how the total areaSAS attribute is stored or how to assign it to a variable. Thank you for your help! Rodrigo. PS. The main goal is to be able to do this without the PDB files and just reading an AMBER topology/trajectory...

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