- Chimera-users - RBVI Mailing Lists

Making a hole in a volume
by Dieter Blaas 01 Jul '14

01 Jul '14

Hi, I am trying to make a small hole in a volume with 'erase octant' but either it cuts away some of the volume at the wrong place or the hole created is much bigger than the green box. Sometimes it does not do anything until I make the box bigger. What might I am doing wrong ? (chimera 1.6.2) Thanks, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Re: [Chimera-users] Fo-Fc electron density maps
by Oliver Clarke 30 Jun '14

30 Jun '14

Actually adding a second arg works well, thanks! So now I have: alias normalize_to_rms vop scale $1 rms 1 modelID $2; close $1; volume $2 capfaces false style mesh meshlighting false squaremesh false color blue; sop cap off alias split_diff_map vop scale $1 rms 1 modelID $2; close $1; volume $2 capfaces false style mesh meshlighting false squaremesh false level -3 color red level 3 color green; sop cap off Where the first one just normalizes to rms and colors blue, and the second one also normalizes but creates two appropriately colored contours, and I can call these as e.g. split_diff_map #0 #1, where #0 is the input map number and #1 is the desired output map number. Cheers, Oliver. On Jun 30, 2014, at 5:06 PM, Tom Goddard <goddard(a)sonic.net> wrote: > Making a macro create map #1000 does not work well, since the second time you use it it will try to make another model #1000. You could add a second argument to your macro that specifies the output model number. Or you make your macro that sets all the volume settings (mesh, capfaces, …) take a model number. None of the choices is very good. > > Tom > > On Jun 30, 2014, at 2:01 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > >> Ah right - that’s okay then, I can just assign it to modelID 1000 then, on the assumption that I’ll never have 1000 models open at the same time. >> >> Thanks! >> >> Oliver. >> On Jun 30, 2014, at 4:59 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >>> There is no special variable to indicate the last created map for use in Chimera commands. In a vop command you can include an option “modelId #5” to assign the id number of the new model. So your macro could take the model id you want for the new map. If you use the vop (volume operation) command to create a new map and don’t specify the modelId option then the new map has the lowest unused model number. There are no output values assigned to variables in the Chimera command language, so it is quite limited. >>> >>> Tom >>> >>> >>> On Jun 30, 2014, at 11:32 AM, Oliver Clarke wrote: >>> >>>> Thanks Tom and Elaine, that’s very helpful! >>>> >>>> While we’re on the topic of macros/aliases, is there any way to refer to the model ID of an output map of a command as a variable in an alias? >>>> >>>> For example, in the normalize_to_rms macro below, I would prefer to apply all the volume settings to just the map I am normalizing, rather than all open maps, but I can’t predict the model ID of the output map because it depends on how many maps I have open. >>>> >>>> This would be handy for stringing together multiple map/model manipulations in a single macro - e.g. to normalize a map to rms, generate two contours and color them appropriately, without disturbing any other open maps. >>>> >>>> Cheers, >>>> Oliver. >>>> >>>> On Jun 30, 2014, at 2:00 PM, Tom Goddard wrote: >>>> >>>>> Hi Oliver, >>>>> >>>>> To simplify your Chimera macros a bit you can put multiple options in one volume command. Instead of >>>>> >>>>> volume # capfaces false; volume # style mesh; volume # meshlighting false; volume # squaremesh false >>>>> >>>>> you can change settings for all open maps with >>>>> >>>>> volume # capfaces false style mesh meshlighting false squaremesh false >>>>> >>>>> Tom >>>>> >>>>> >>>>> On Jun 28, 2014, at 3:14 PM, Oliver Clarke wrote: >>>>> >>>>>> Dear Egor, >>>>>> >>>>>> In addition to Elaine’s suggestion of unchecking “Cap high values at box faces", I use the following aliases to make difference maps more familiar in style to a crystallographer: >>>>>> >>>>>> First, to just normalize the map to RMS (as per coot etc) and adjust to get a mesh, turn capping, mesh lighting off etc: >>>>>> >>>>>> alias normalize_to_rms vop scale $1 rms 1; close $1; volume # capfaces false; sop cap off; volume # style mesh; volume # meshlighting false; volume # square mesh false >>>>>> >>>>>> Second, to split the map into two maps (one positive, one negative), which can then be colored green and red respectively: >>>>>> >>>>>> alias split_diff_map vop threshold $1 minimum 0; vop threshold $1 maximum 0; close $1; sop cap off; volume # style mesh; volume # meshlighting false; volume # squaremesh false; >>>>>> >>>>>> I add these two lines in a “chimera_aliases.com” file, which you can tell Chimera to read at startup under Favorites—>Preferences—>Command Line. >>>>>> >>>>>> You can then run these commands from the chimera command line, e.g. normalize_to_rms #1 or split_diff_map #1 if your map number is 1. Then just adjust the contours and colors in the volume viewer and you are good to go. >>>>>> >>>>>> I don’t know how to automatically color the resultant maps, because there does not seem an obvious way to predict their model numbers, but I am sure there is a way to do that too, perhaps via some python trickery. >>>>>> >>>>>> This is all kind of a work around of course - there may be a way to color a map by density value (such that all positive regions are green, and all negate regions are red), but I couldn’t figure out how to do it. >>>>>> >>>>>> Best, >>>>>> Oliver. >>>>>> _______________________________________________ >>>>>> Chimera-users mailing list >>>>>> Chimera-users(a)cgl.ucsf.edu >>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>>> >>>>> >>>> >>>> >>> >> >> >

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Re: [Chimera-users] Fo-Fc electron density maps
by Oliver Clarke 30 Jun '14

30 Jun '14

Dear Egor, In addition to Elaine’s suggestion of unchecking “Cap high values at box faces", I use the following aliases to make difference maps more familiar in style to a crystallographer: First, to just normalize the map to RMS (as per coot etc) and adjust to get a mesh, turn capping, mesh lighting off etc: alias normalize_to_rms vop scale $1 rms 1; close $1; volume # capfaces false; sop cap off; volume # style mesh; volume # meshlighting false; volume # square mesh false Second, to split the map into two maps (one positive, one negative), which can then be colored green and red respectively: alias split_diff_map vop threshold $1 minimum 0; vop threshold $1 maximum 0; close $1; sop cap off; volume # style mesh; volume # meshlighting false; volume # squaremesh false; I add these two lines in a “chimera_aliases.com” file, which you can tell Chimera to read at startup under Favorites—>Preferences—>Command Line. You can then run these commands from the chimera command line, e.g. normalize_to_rms #1 or split_diff_map #1 if your map number is 1. Then just adjust the contours and colors in the volume viewer and you are good to go. I don’t know how to automatically color the resultant maps, because there does not seem an obvious way to predict their model numbers, but I am sure there is a way to do that too, perhaps via some python trickery. This is all kind of a work around of course - there may be a way to color a map by density value (such that all positive regions are green, and all negate regions are red), but I couldn’t figure out how to do it. Best, Oliver.

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Calculating ASA for side chain
by saadraza＠bs.qau.edu.pk 29 Jun '14

29 Jun '14

Respected Admin I would like to know if there is any way to modify the calculation of Accessible Surface Area (ASA) to calculate only the ASA for the side chain or a particular group of atoms in chimera. If not possible could someone guide me to some other tool. I will be obliged if someone sort this problem for me Regards Saad Raza

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Fo-Fc electron density maps
by Egor Tchesnokov 28 Jun '14

28 Jun '14

Hello, Is there a way to display Fo-Fc electron density maps so that "red/negative" and "green/positive" densities are displayed at the same time. Thank you Egor

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Urgent: surface calculus
by Olivier Sire 27 Jun '14

27 Jun '14

Hello, I am in a hurry to generate a surface object with 2FJG complex to be exported in a STL format for 3D printing. This item will be presented for a local event organized by the Ligue contre le Cancer. I have download Chimera as absolute beginner and I am facing a need for splitting the (too big ?, multi-chain) complex. The function Action / Surface / show generates the splitting solution. Could you help me and guide me ? Thanks in advance Regards Olivier Sire -- *Olivier SIRE * / Professeur à l'Université de Bretagne-Sud / ------------------------------------------------------------------------ Laboratoire d'Ingénierie des Matériaux de Bretagne Campus de Tohannic BP575 56017 VANNES cedex Tél. 02 97 01 71 48 Fax. 02 97 01 70 70 Mob. 06 89 48 25 24 olivier.sire(a)univ-ubs.fr UNIVERSITÉ DE BRETAGNE-SUD http://www-limatb.univ-ubs.fr/ <http://www.univ-ubs.fr/>

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Build a quadruplex
by sette＠uniroma2.it 26 Jun '14

26 Jun '14

Dear all, Im interested to create a rough model of a quadruplex molecule using a specific sequence. One possibility could be to load a pdb structure of a quadruplex and « mutate » each nucleotide with the correct one. Is this feasible with Chimera ? Alternative suggestions are appreciated as well. Thanks for your help, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it e-mail: m77it(a)yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 www.rete29aprile.it ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

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Rainbow by secondary structural element?
by Oliver Clarke 26 Jun '14

26 Jun '14

Hi all, Currently, the rainbow function can operate at the levels of per residue, per chain or per model. I was wondering whether it would be feasible in a future release to add an additional level, coloring per secondary structural element? This would be particularly handy for structures of membrane proteins, where it is often desirable to color each helix/strand a different color, while not varying the color along the helix (and not coloring residues in loops etc). Even better would be to have separate “rainbow helix” “rainbow strand” and “rainbow secstruc” commands for finer control, but this is probably not really necessary. Cheers, Oliver.

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Color by height from surface?
by Oliver Clarke 25 Jun '14

25 Jun '14

Hi all, I’m wondering if there is any way to use scolor to color by height from another surface rather than from a plane, axis or point? Specifically, I’d like to color a molecular surface by distance from the surface of the low-res model generated using multi-scale models, in order to highlight cavities in the surface of the protein. Best, Oliver.

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Chimera scripting with --nogui can't write pdb files
by rswett＠chem.wayne.edu 24 Jun '14

24 Jun '14

Hey guys, i've been trying to put together a command line only set of scripts that will do some selection processing and save a pdb without going through the gui. If I use the command chimera --nogui --script close.py pdb1.pdb pdb2.pdb where close.py contains select #0 za<3 & #1:HOH write selected 1 output.pdb I should get the residues that match that selection criteria saved as the pdb output.pdb, correct? I get SyntaxError: invalid syntax for line 2 even though this works OUTSIDE a script. as in, if I just run chimera command line and enter those commands sequentially, it works. I also noticed that within the gui I need "#1" and outside it only works with '1" as the model number. I've also tried doing this with a python script: chimera --nogui --nostatus --script "close.py pdb1.pdb pdb2.pdb output.pdb" this should pass whatever I enter as $1 $2 $3 as arguments to my script, correct? So close.py for this version contains open (sys.argv[1]) open (sys.argv[2]) select #0 za<3 & #1:CVX write selected 1 (sys.argv[3]) which also pukes on the pdb write. I couldn't find any other way to write a pdb using python syntax, I assume the way i'm doing it is wrong, but I couldn't find a write.pdb function during my digging. Does anyone have suggestions for writing a pdb based on a selection without going through the gui? I plan on batching this up for a huge number of files and directories and going through the gui would be far too time consuming. Rebecca

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