- Chimera-users - RBVI Mailing Lists

Python Script to Find Contact Area Between 2 Proteins
by Kevin Wang 29 Aug '19

29 Aug '19

Hi, I am writing a python script to find the area between 2 proteins using the contact_area python command below. def contact_area(p1, p2, d, color = None, offset = None, slab = None, smooth = False, optimize = True): Is there a specific object for p1 and p2 and if so how do I get it? My current code is as follows: import os import chimera from Measure import contactarea from chimera import * Path = "/Users/kevinwang/desktop/VEGFR_NO_LIGAND/results/clustering/pdbfit/split" filelist = os.listdir(Path) for x in filelist: #if x.startswith("trp.pdb."): if (x == "trp.pdb.00001"): print x opened = chimera.openModels.open(x, type ="PDB") runCommand('surface') y = contactarea.contact_area('0.1', '0.2', 2.5) text_file = open("buriedArea.txt", "w") text_file.write(y) text_file.close() The error message I am getting is as follows: AttributeError: 'str' object has no attribute 'geometry' File "/Applications/Chimera.app/Contents/Resources/share/Measure/contactarea.py", line 8, in contact_area v1, t1 = p1.geometry How should I be passing in my arguments? Best, Kevin

2 3

code 256
by Aleksandra Jarmołowicz 29 Aug '19

29 Aug '19

Dear Sir or Madame, During chimera-1.13.1-linux_x86_64 installation process I have found some difficulties. I have not found any solutions on your website. After running instalation an error appears : ERROR in chimera_final_install: unable to install deskop icon: result code from installer: 256 I would be very greatful for any help. Kind regards, Aleksandra Jarmołowicz -- Aleksandra Jarmołowicz Ph.D. Student Department of RNA Structural Genomics Institute of Bioorganic Chemistry Polish Academy of Sciences Z. Noskowskiego str. 12/14 61-704 Poznań Phone: +48 61 852 8503 ext 143 ajarmolowicz(a)ibch.poznan.pl

2 1

Can multiple marker sets be batch-saved into individual .cmm files?
by Jun Ha Song 28 Aug '19

28 Aug '19

Dear RBVI, I need to save around 340 market sets into individual .cmm files, 1 .cmm for each marker set I have in my Chimera session. I have been looking at UCSF Chimera documentation for some time ( https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/…) and I wanted to ask if multiple marker sets (each with its own unique model ID) can be saved in single batch command line. Is there a possibility of specifying commands like *save* or *write* or *export* with atom specification of all the model that I want to save to make Chimera save all my 340 marker sets as their individual .cmm files? I was hoping that I could simply use something like *save #1-340 individual UseModelIDasFilename format .cmm directory E:\LBNL\Individual_Models* to make it happen, but all the commands that I thought of as potential candidate for batch-save command doesn't mention whether it can work with volume tracer's "Save current marker set as...". or, if I can use Volume Tracer's "Save current marker set as..." using a script, I could handle this by making myself very simple macro, but I don't know whether volume tracer's codes would allow some quick script to substitute its "Save current marker set as..." function. So, in summary, I wanted to know if... Q1 : Is there a command in UCSF Chimera that allows batch saving multiple market sets as individual .cmm files? Q2 : Can Volume Tracer's "Save current marker set as..." function be used by using some kind of script? Sincerely, Junha Song.

2 1

Get map contour level with python script or command
by Kyle Morris 28 Aug '19

28 Aug '19

Dear chimera users and dev, Is there a chimera or python command that can report the current contour level of a volume that is in model number #n back to the reply log or equivalent? I want to do this after executing 'volume #n sdLevel 3’ such that I can programmatically retrieve the contour level associated with a particular sigma level of a currently loaded volume. Apologies if in my searching I have missed this on the boards, I think this is a novel question though. Thanks as always for your help. Best wishes, Kyle

3 2

How to read a volume in python script
by Huiya Zhou 28 Aug '19

28 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

3 2

Chimera Error
by Ryan Harlich 27 Aug '19

27 Aug '19

Hi Chimera, I am having trouble opening a pdb file. I get the following error: ValueError: can’t normalize zero length array File \Chimera1.13.1\share\chimera\tkgui.py, line 3030, In showLabelBalloon Objs = self.viewer.pick(event.x, event.y) All other PDBs are opening so I am not sure why this one won’t open. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

2 1

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

2 1

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

2 1

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

2 2

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

2 1