- Chimera-users - RBVI Mailing Lists

Support chimera
by Jose Alirio Mendoza Mesa 03 Sep '19

03 Sep '19

Hi there, my name is Jose Alirio Mendoza. Currently, I am carrying out my PHD thesis in which I am using the chimera program to show the tomography results. Nevertheless, I am being presented some problems when trying to measure my particle in Chimera. The file of my product is “mrc” and I have been investigating about chimera usage where I have realized that the file must be “pdb” for the program to recognize it. I do not really know how to convert my molecule to the required file, and I guess that is the problem by which I cannot measure the distance of my particle. When I click “tools – structure analysis – distance” it does not appear the code of my molecule as in picture below [image: imagen.png] This is my particle and what I get when using the tool for measuring. I have other three tomography for one publication. [image: imagen.png] There is not any code in the tool square and that is why I guess to no be able to measure the particle. Other tool I tried to use is the scale bar, however the value of it is not according to my calibration. [image: imagen.png] How may I change that calibration? In our research group we want the publish the articles citing chimera as visualization tool so we would really appreciate your help. Here is attached the file we have worked in chimera. pollo 13.mrc <https://drive.google.com/a/unal.edu.co/file/d/1cAs2g1kP88o8im65xuTbOz11o9pk…> -- *Qco. JOSE ALIRIO MENDOZA MESA* Candidato a Doctor en ciencias Universidad Nacional de Colombia. 3165000 Ext. 14475 *LABORATORIO DE CATALISIS HETEREOGENEA*

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Re: [Chimera-users] code 256
by Greg Couch 30 Aug '19

30 Aug '19

Like I said before in http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-August/016113.html, you need to use the daily build of Chimera. Go the Chimera download web page, http://www.cgl.ucsf.edu/chimera/download.html. Scroll down past the 1.13.1 downloads, and pick the 64-bit Linux daily build version to download. Then install it. When 1.14 comes out, it will not have this problem. -- Greg On 8/29/2019 11:22 PM, Aleksandra Jarmołowicz wrote: > > I am using Ubuntu 19.04. So what can I do to use Chimera with this > version? Before update of the system programme runs well. > > 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 <mailto:ajarmolowicz@ibch.poznan.pl>

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Buried_area python function
by Kevin Wang 29 Aug '19

29 Aug '19

Hi, I am trying to use the buried_area function below. What are the arguments that I need to pass in? def buried_area(operation, atoms1, atoms2, probeRadius = 1.4, vertexDensity = 2.0): My current code is as follows: #calculate buried area import os import chimera import xlsxwriter from Measure import measure from chimera import * workbook = xlsxwriter.Workbook('contactArea.xlsx') worksheet = workbook.add_worksheet() Path = "/Users/kevinwang/desktop/VEGFR_NO_LIGAND/results/clustering/pdbfit/split" i = 0 filelist = os.listdir(Path) for x in filelist: if x.startswith("trp.pdb."): #if (x == "trp.pdb.00001"): opened = chimera.openModels.open(x, type ="PDB") chimera.update.checkForChanges() try: runCommand('surface :286-596') runCommand('surface :899-1230') y = measure.buried_area() worksheet.write(i,0,x) worksheet.write(i,1,y) except: worksheet.write(i,0,x) worksheet.write(i,1,"ERROR") i = i + 1 print("Processed: " + x) print("Total #: " + str(i)) runCommand('close all') chimera.update.checkForChanges() workbook.close() Best, Kevin

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copy transformation between volumes
by Oleksiy Kovtun 29 Aug '19

29 Aug '19

Dear community, I need your advice on the following problem. I align map #1 to the reference volume using fit command, and then need to confer this transformation to map #2. This could be done by using matrixcopy command. However in this particular case #1 has twice larger voxel size than #2. It is understod, that since transformation matrix describes shifts in non-scaled pixels, I can not use matrixcopy command. Is it correct to scale translations (column 4) in the fit matrix for #1 and apply it to #2 with matrixset command? Thank you and best regards, Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

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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

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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

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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.

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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

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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

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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

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