October 2015 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

4 6

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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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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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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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

4 7

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

3 2

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.

2 7

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.

2 1

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

1 0

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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Chimera-users October 2015