[chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax

Tue Feb 2 08:27:18 PST 2021

Hi Yeping,
Since  you didn't say what structure you were using, I just tested coloring by your entropy attribute file on some other structure.  Probably my test structure did not contain the residue numbers with 0.3, so the coloring did not look interesting.

ChimeraX does not yet have the ability to draw a color key (color gradient bar with values marked), although it is being worked on now.  Currently if you still want to use ChimeraX for the main image, you could use Chimera to draw the color key separately and then put them together in an image editing program (gimp, photoshop, ...).

I hope this helps,
Elaine

> On Feb 2, 2021, at 12:03 AM, sunyeping <sunyeping at aliyun.com> wrote:
> 
> Hi Elaine,
> 
> Thank you for you help. I will send chimerax questions to chimerax mail list next time.
> 
> By changing the match mode from "1-to-1" to 'any', I can also color the protein according to the entropy.txt file. 
> If you recheck the entropy.txt file you will find that there are quite a few residues have an entropy vavle around 0.3, in addition to the 0.788 residue.
> Could you tell me how to generate a color gradient bar base on the entropy values in the entropy.txt file in chimerax?
> 
> Best regards,
> Yeping
> 
> ------------------------------------------------------------------
> From:Elaine Meng <meng at cgl.ucsf.edu>
> Send Time:2021年1月28日(星期四) 00:44
> To:孙业平 <sunyeping at aliyun.com>
> Cc:ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> Subject:Re: [Chimera-users] how to color an model by an attribute in chimerax
> 
> Hi Yeping,
> **Please send ChimeraX questions to the chimerax-users at cgl.ucsf.edu address, *not* to chimera-users at cgl.ucsf.edu, because that makes people confused about which program we are talking about.
> 
> Two more thoughts about your file:
> 
> (1) you need to make sure the residue numbers in the file all match to your structure.  I don't know which structure you are using so when I test it on some other structure that doesn't have all the same residue numbers, it does not work unless I change the match mode from "1-to-1" to "any".  You might want to try using match mode "any".
> 
> (2) looks like one residue has a high value 0.788 and all the others are very close to zero, so when I color the whole range the structure is all the same color (used for the low end) except for the one high-value residue.  E.g. coloring by attribute entropy using palette blue-white-red makes the whole structure blue except for one residue red.  
> 
> Elaine
> 
> > On Jan 27, 2021, at 8:25 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > 
> > Hi Sun Yeping,
> > To use the "open" command to open defattr format you need ChimeraX daily build from Oct 30, 2020 or newer.  Or if you are using ChimeraX 1.1, you can use the "defattr" command to open the file.  Older ChimeraX than version 1.1 cannot read this file type at all.  Changes and approximate dates are given in the Change Log:
> > 
> > <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>
> > 
> > The format is described here:
> > <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html>
> > 
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.                       
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> > 
> > 
> >> On Jan 27, 2021, at 1:04 AM, sunyeping <sunyeping at aliyun.com> wrote:
> >> 
> >> Dear Elaine,
> >> 
> >> Thank you for your reply. The attribute file entropy.txt is available at 
> >> 
> >> https://drive.google.com/file/d/1oG0O4zKqw-uD5SeLTrAu16c3Jh8m3LG5/view?usp=sharing
> >> 
> >> Could you please help check whether the format is correct"?
> >> 
> >> I cannot figure out how to open this attribure file in chimera. When I input "open entropy.txt format defattr" in chimerax, I get the following error message:
> >> 
> >> Invalid "format" argument: Should be one of 'aln', 'amira', 'apbs', 'bild', 'brix', 'ccd', 'ccp4', 'cellpack', 'cmap', 'cmd', 'collada', 'compiled python', 'cube', 'dcd', 'delphi', 'dicom', 'dock', 'dsn6', 'dv', 'emanhdf', 'fasta', 'fsc', 'gltf', 'gopenmol', 'hdf', 'hssp', 'html', 'ihm', 'images', 'imagic', 'imod', 'imodmap', 'ims', 'macmolplt', 'markers', 'mmcif', 'mmtf', 'mol2', 'mrc', 'msf', 'netcdf', 'obj', 'pdb', 'pdbqt', 'pfam', 'pif', 'pir', 'positions', 'priism', 'profec', 'pseudobonds', 'python', 'rsf', 'sdf', 'segger', 'session', 'sff', 'situs', 'smiles', 'spider', 'stl', 'stockholm', 'storm', 'swc', 'tom_em', 'trr', 'uhbd', 'uniprot', 'vtk', 'web fetch', 'xplor', or 'xtc'
> >> 
> >> Could you tell me what is the correct way to open the file?
> >> 
> >> Thank you,
> >> Best,
> >> Yeping
> >> ------------------------------------------------------------------
> >> From:孙业平 <sunyeping at aliyun.com>
> >> Send Time:2021年1月26日(星期二) 11:53
> >> To:chimera-users <chimera-users at cgl.ucsf.edu>
> >> Subject:[Chimera-users] how to color an model by an attribute in chimerax
> >> 
> >> Dear all,
> >> 
> >> I wish to color an model  by an attribute in chimerax. The attribute is the entropy which is calculted by an external software. I wrote the entropy values of each residue in a text file (attr.txt) like the following:
> >> 
> >> attribute: entropy
> >> match mode: 1-to-1
> >> recipient: residues
> >> :1 0.0
> >> :2 0.0014948
> >> :3 0.0090952
> >> :4 0.0004805
> >> :5 0.1102497
> >> :6 0.0095258
> >> :7 0.0008226
> >> :8 0.0042205
> >> :9 0.0037255
> >> :10 0.0006678
> >> :11 0.0027988
> >> :12 0.0193925
> >> :13 0.0153925
> >> :14 0.0052115
> >> :15 0.0020136
> >> ..........
> >> 
> >> However, when I input the command "color byattr attr.txt", I get the following error information:
> >> "No known/Registered attribute attr.txt"
> >> 
> >> Could anyone tell me what is the correct way to do this?
> >> 
> >> With many thanks.
> >> 
> >> Best regards