August 2019 - Chimera-users - RBVI Mailing Lists

Fw: Open MTZ file
by Williams, Joanne 20 Aug '20

20 Aug '20

Hello! Can you help with the inquiry below? thanks, Jo ________________________________ From: Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> Sent: Thursday, February 22, 2018 5:01 AM To: chimera(a)cgl.ucsf.edu Subject: Open MTZ file Is it possible to open an .mtz file in Chimera? ~~~~~~~~~~~~~~~~~~~~~~~~~~ Sharyn A. Endow, PhD Professor of Cell Biology, DUMC Professor of NBD, Duke-NUS PO Box 3709 450 Sands Bldg/Research Drive Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

5 6

Fwd: Downloading HIV PDB 3j3q?
by Elaine Meng 13 Jan '20

13 Jan '20

> > From: Divjak Maja <Maja.Divjak(a)petermac.org> > Subject: Downloading HIV PDB 3j3q? > Date: April 1, 2019 at 5:23:39 AM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > > Hi Elaine, > > It's me again! Hope you had a nice weekend... > > I'm having some trouble downloading the HIV capsid file, PDB 3j3q. When I try to import it to Chimera it begins downloading, but the molecule never quite appears, even though it ends up in the entry list. The screen stays blue like it has yet to be uploaded. If I try to upload it from the list, again, nothing appears. I realise the molecule is very large, but I think I'm missing something important here? > > Thanks so much for your help, as always, > > Maja > > Dr Maja Divjak > BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) > Biomedical Animator > Office of Cancer Research > Hi Maja, (forwarding to the address that should be used for for Chimera questions) It is probably just too big for the memory on your computer to open this structure in Chimera. Depending on what you’re trying to do with this capsid, maybe you could try using ChimeraX instead of Chimera. It handles large structures much more efficiently, but it does not have the same set of features as Chimera. <http://www.rbvi.ucsf.edu/chimerax/index.html <http://www.rbvi.ucsf.edu/chimerax/index.html>> If you are just trying to get the atomic coordinates of the entire capsid, they are already in the file(s) you could download directly from the RCSB PDB without using any visualization program. <https://www.rcsb.org/structure/3j3q <https://www.rcsb.org/structure/3j3q>> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 5

Fetch by EMDB via GUI downloads first where before uncompressing in users downloads directory
by Ryan Harlich 08 Nov '19

08 Nov '19

Hi Chimera, If I fetch by EMDB via GUI and it downloads then decompresses and freezes where did it go? I know when it is done it goes to my download directory, but where does the gz get downloaded to and where does the partial uncompressed file end up. I cannot find ~5-~10 GB of this lost file. It was ~5 GB gz file so I think the gz is still on my computer. I searched for it to and my computer said no results found so I am not sure if it is named something else when you fetch by EMDB. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

5 5

Way to compute residue wise RMSD using python script in chimera:
by Kamalesh Damodaran 09 Sep '19

09 Sep '19

Dear sir/madam, I would like to superimpose the two structures and compute the residue wise RMSD values. With Gui support in chimera, I opened the two structures and used Matchmaker to superimpose two structures. In Matchmaker, I checked the box 'Show pairwise alignment(s)' and click Apply, subsequently it displays MultAlignViewer dialogue box, where --> Headers --> RMSD : backbone --> Save --> filenamegiven. This process would give me residue wise RMSD score only for backbone atoms in .hdr format. I wants to write python script to do the same, so that I will compare large number of structures, and my script is able to perform till the procedure of superimposition using matchmaker and display MultAlignViewer dialogue box. I don't know the way to store the RMSD : backbone and RMSD : calpha in .hdr format using python script through chimera. Can some one please help me in this. The reason why I specifically want to do in this approach is, because among the two structures, some residues of one structure is missing. Since this approach will compute RMSD only for the matching residues, I am interested in this. Hope my question is not confusing. Thanks in advance. Best regards, Kamalesh D.

2 3

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>

1 0

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

2 1

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

2 1

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

Chimera-users August 2019