- Chimera-users - RBVI Mailing Lists

Subtracting the difference in EM volumes
by Y. Mutum 27 Aug '19

27 Aug '19

Hi Is there a way to subtract the non-overlapping bits and retain only the overlapping volumes between 2 EM density maps in Chimera? I have tried the vop subtract command, but it only seems to subtract the overlapping bits and not the inverse of it (non-overlapping bits)? Sorry, if I have missed it. Thanks Yilog

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Divided the Volume Data into two parts
by Huiya Zhou 23 Aug '19

23 Aug '19

Hello, I would like to divided a density map (volume data) into two parts. For example, the size of the whole density map is 320*320*320. I want to get one part which covers the region from (i,j,k) to (x,y,z), e.g. from (0,0,0) to (100,100,100). The rest is the other part. The transparency for the first part is 0 and for the second part is 0.5. And I still want to get the histogram of the first part. How could I achieve this in a python script? Actually, I want to get the histogram of different regions. I plan to run a loop for different regions (Change the (i,i,k) and (x,y,z) for the first part). Could I save all of the histograms in one file which is not a window of the Chimera but a picture. Best, Huiya

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Selecting bonds/pseudobonds with a cutt-off distance
by Yasser Almeida Hernández 23 Aug '19

23 Aug '19

Hi all, how can I select bonds/pseudobonds with a cutt-off distance, say bonds/pseudobonds with more than/less than X? Thanks in advance, Yasser

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回复： scipy problem
by William 23 Aug '19

23 Aug '19

Dear Eric, I have tried the instructions following the FAQ, but there is another problem. The scipy installed successfully. However, it installed a higher version of the numpy when installing scipy. And the older version of numpy is still in. The chimera can not work. Anyway, thanks a lot. ------------------ 原始邮件 ------------------ 发件人: "Eric Pettersen"<pett(a)cgl.ucsf.edu>; 发送时间: 2019年8月20日(星期二) 凌晨1:46 收件人: "William"<3121437640(a)qq.com>; 抄送: "chimera-users"<chimera-users(a)cgl.ucsf.edu>; 主题: Re: [Chimera-users] scipy problem Hi William, I don’t know why Jaime’s instructions don’t work. Maybe he can follow up. Regardless, we have our own instructions for installing pip (and pip-able packages like scipy). It’s in the Chimera Programming FAQ. Question 3b. If those instructions don’t work, please let us know. —Eric Eric Pettersen UCSF Computer Graphics Lab

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How to read a volume in python script
by Huiya Zhou 22 Aug '19

22 Aug '19

Hello, I am trying to use UCSF Chimera to analysis cry-EM density maps. I would like to read a density map (for example: a .mrc file) in python script and get the array (or a three dimensional matrix) of all voxels of this density map. How could I realize this? By the way, I tried to learn some basic chimera functions which can be used in python on this website: https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html> However, it seems this website can’t be opened and it shows me a blank page. Best, Huiya

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copy/combine molecular models
by Rui Chen 22 Aug '19

22 Aug '19

Hello, I am working on a homodimer. I modelled loops of each chain one by one. I chose the best loops for each chain. Now I want to save them as a pub file. Please see the following screenshot. How to decide the new model's ID? I know the coordinate system is the reference coordinate, how do I decide which chain to use as the reference chain? Should I choose rename them uniquely? Looking forward to hearing from you. Thank you. [image: Screen Shot 2019-08-22 at 12.01.28 AM.png] Best regards, Rui

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how to guess ligand's net charge?
by Thomas Evangelidis 21 Aug '19

21 Aug '19

Greetings, How does Chimera guess the net charge of a ligand when prompted to select the charge type (AM1-bcc or Gasteiger)? I am doing high throughput protein-ligand MD simulations and would like to know which open source library Chimera uses for this task. Thanks in advance. Thomas -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: tevang3(a)gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/

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color by zone in chimeraX
by Pranav Shah 20 Aug '19

20 Aug '19

Hi Elaine and Co., I am trying to color a virus map with the relevant pdb file, the series of commands I am running are as follows, open virus.mrc open virus.pdb color /A plum target c color /B lightgreen target c color /C dodger blue target c color zone #1 near #2 dist 3 However, the resultant surface is rendered in splotches of red and blue, which leads me to think the it is coloring the surface using atom type. Could you tell me how I can get Chimera X to color the surface using the colors of the chains only? FYI, color by zone works flawlessly in chimera. Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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scipy problem
by William 19 Aug '19

19 Aug '19

Hello, I tried to install scipy in chimera python following the steps below: When I tried the third step, it raised midaserror. The error is as follows： Is there anything wrong with my path? Thanks.

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Match showmatrix true motion in original coordinates
by Ahmad Khalifa 13 Aug '19

13 Aug '19

Hi, Running match showmatrix true, gives two matrices. What's the difference between the two? I already saved the file after fitting it so it should have only one set of coordinates, its original coordinates?! Regards Motion of #76 in #2 coordinate system Matrix rotation and translation 0.99998889 -0.00169318 0.00440013 -1.57825672 0.00165962 0.99996960 0.00761849 -4.96792547 -0.00441290 -0.00761111 0.99996130 169.74075587 Axis -0.85023004 0.49200930 0.18717833 Axis point 0.00000000 21533.64775327 2718.66675667 Rotation angle (degrees) 0.51315730 Shift along axis 30.66940614 Motion of #76 original coordinates in #2 coordinate system Matrix rotation and translation 0.78916125 0.61416829 0.00467203 -143.02960322 -0.61417583 0.78916918 0.00023085 242.10381668 -0.00354524 -0.00305162 0.99998906 98.04867640 Axis -0.00267220 0.00668954 -0.99997405 Axis point 281.92931592 330.08522286 0.00000000 Rotation angle (degrees) 37.89294229 Shift along axis -96.04436567

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