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how to copy partial charges from a .mol2 file to another
by Thomas Evangelidis 29 Feb '12

29 Feb '12

Dear Chimera community, Is there any straight forward way to copy the partial charges from one .mol2 file to another? Thanks in advance. Thomas -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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partial conservation coloring
by Eric Pettersen 28 Feb '12

28 Feb '12

Jill Voreis wrote: > I'm trying to use chimera to show conservation maps. Using pdb files > that I fetch from the database using the pdb id number and > alignments created in clustal that contain the sequence of the pdb > file, I select render by conservation. For some reason, the > conservation colors only go onto my model when it's in ribbon form. > When I try to show the surface representation or use spheres so that > I can use commans to show the SAS, the colors of my model do not > match the conservation model but rather are stuck on some sort of > coloring scheme related to the compounds that are there. The > majority of the map looks brown, like the default color before > rendering by conservation. If you could help me, I'd really > appreciate it! Hi Jill, There are a few possibilities here, though it's impossible to be certain what the problem without access to a concrete example. My best guess is that much of the surface region of your protein is poorly conserved and those areas have columns where the rows are more than 50% gap characters. For such columns no conservation score is assigned. That means that when you use Render By Attribute with default settings, those atoms / surface parts will retain their original colors. If in Render By Attribute you use the "No-value color" color well to assign a color to such regions (perhaps gray) you will be able to tell if this is what is happening. Two other possibilities are that you don't have the "Color atom" and "Color surfaces" check boxes checked [though I image you would have noticed this!] or that your protein has multiple chains and that only one is associated with the alignment and only that one is getting colored. If none of these are "it", if you can provide me with a specific example so I can reproduce the behavior then I will investigate. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Not crossfade but coinciding bond command...
by Kevin D. Walker 28 Feb '12

28 Feb '12

I temporarily disabled a bond command and found this to be the cause of the selected bond problem I am having. I don't think crossfade has anything to do with it.

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Animate a Reacton Mechanism?
by Kevin D. Walker 28 Feb '12

28 Feb '12

I constructed a movie for the first part of a reaction mechanism (substrate docking). I would like the animated mechanism to continue as follows. The substrate donates a proton to a tyrosine residue of the enzyme, forming an intermediate. The intermediate rotates 180 (I have accomplished this part) and the proton rebounds to the intermediate forming a new product, which is released. I can animate the product release -- it's the reverse of substrate docking. The part of the animation I cannot envisage is how to smoothly show or morph the bond transitions (bond breaking and making) during the reaction progression. IAny advice on whether Chimera or other ancillary software can do this is appreciated.

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using CalcAttr from a Python script
by Roger L. Chang 27 Feb '12

27 Feb '12

Hi, 1) I need to get residue.areaSES for two separate selections (all polar amino acids and all nonpolar amino acids). I have successfully generated a list of residue.areaSES using the GUI simply by selecting the residues of interest and then using the attribute calculator typing "residue.areaSES" in the formula box of the Attribute Calculator, which outputs the list to the Reply Log. This is the data that I need, but I need to get it for >2000 PDB structures and would like to automate this analysis through a Python script. I am somewhat new to Python and Chimera and don't yet know all the ins and outs yet. I dug through the code and found a method "getResidueAttr" in the "ResidueDataWrapper" class from "CalcAttr". This seems to be what I need, but I don't know the proper syntax to call it from my Python script. Could someone please provide an example? 2) I would like to sum the residue.areaSES values once I have them. I tried "sum(residue.areaSES)" in the formula box of the Attribute Calculator in the GUI, but this returns the error "Formula evaluation error: expecting vector argument in function". I'm not sure again on the proper syntax to use "sum()" in the Attribute Calculator. If I knew how to generate/save the residue.areaSES data from the command line, I could just parse the saved file and sum the values in Python. How can Attribute Calculator formulas be used from the command line, and if they can't, how can I save the residue.areaSES data to file from a Python script? Thanks in advance, Roger -- Roger L. Chang Graduate Student Bioinformatics and Systems Biology Graduate Program University of California, San Diego

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Coloring molmap surfaces
by Tom Goddard 24 Feb '12

24 Feb '12

> Greetings Tom > > How can color the molmap surface of certain atoms/residues. > > Many Thanks, Vijay > Hi Vijay, Use the Color Zone dialog to color a molmap surface to match nearby atom colors (menu Tools / Volume Data / Color Zone). You select the atoms you want to use for color (e.g. menu Select / Select All) choose a distance range from those atoms to color in the Color Zone dialog and press the Color button. In Chimera 1.6 (release candidate available on the web) or daily builds there is a command version of color zone. For example scolor #0 zone @ca range 5 says to color molmap surface #0 to match C-alpha atom colors within a distance of 5 Angstroms. To avoid jagged edges in the coloring you should use the molmap gridSpacing option to specify a grid size about 1/5 to 1/10 the map resolution. The default value is 1/3 of map resolution making a fairly coarse surface mesh. Colors are only assigned to the mesh vertices, so a fine mesh is needed for smooth boundaries between different color regions. Tom

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batch peptide builder
by Xiao-Ping Zhang 23 Feb '12

23 Feb '12

Dear Chimera developers, I would like to generate some peptides from a protein sequence. The peptide builder in Chimera is a very nice application. I wonder if there is a stand alone script which I can use to generate series peptides from the command line. Thank you for your help. Xiao-Ping Zhang

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Drawing arrows without using .bild file
by Victor Muñoz 21 Feb '12

21 Feb '12

Dear all, I'm trying to make a script that draws an arrow on every atom and every frame during a trajectory using the MD movie. Right now, the script creates a .bild file to draw the arrows, but it is not a very good approach since it is creating a new file for every frame of the trajectory. I was wondering if there's a way to do the same thing without having to create the .bild file. I already checked the "shape" command but you can´t use it to draw an arrow. Maybe I should make a combination between a cylinder and a rectangle to draw an arrow? Is there any other easy way to do that? Thanks in advance. Kind regards, --

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bug
by Eifler, Jay Q. (UMKC-Student) 21 Feb '12

21 Feb '12

Whew, too much work to get you guys a message. The bug report form was lengthy. Anyway, can't join models in your latest 1.6 version but 1.5 whatever is fine. Should have never updated.

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(no subject)
by Valia Dimitrova 21 Feb '12

21 Feb '12

Hi, I am PhD student, and I am working with program Gaussian, I want ask you some questions. I want to make maps with electrostatic potential, I saw that with this program may be make very beautiful pictures. What type of files I have to have, so I can do these pictures? I have ".fchk" files and ".cube" files. May I use them to make this? I will be very appreciated if some one can help me. thank you in advance Valia Nikolova

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