- Chimera-users - RBVI Mailing Lists

Max 100 residues for local bug?
by Danilo Boškovic 16 Sep '19

16 Sep '19

Dear caretakers, I tried to do autodock vina but as soon as i did i got an error that i can only do max 100 residues. I use a local installation of AVina. Is this a bug or is there somewhere something im missing? 41965 build number 1.13.1 version Sincerely, D. B.

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Where is the radius.nc map file in the Semliki Forest virus?
by sunyeping 16 Sep '19

16 Sep '19

Dear everyone, The Semliki Forest virus tutorial (https://www.cgl.ucsf.edu/chimera/data/tutorials/semliki/semliki.html) mentioned a radius.nc which is used for visualization of the layer. However, the tutorial doesn't describe where the reader can download it. Do you know where to get thid file? Thank you in advance. Yeping Sun

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Re: [Chimera-users] Electrostatic potential molecular surfaces
by Elaine Meng 11 Sep '19

11 Sep '19

Hi Fernando, Our resources don’t allow spending much time on consulting with individual research projects, sorry, and I can only answer mostly as it pertains to Chimera as I don’t know the details of parameters developed by other people or other programs. Also Chimera questions should be sent to this mailing list instead of to me directly so that other people can also benefit, unless private data are discussed or attached. You found an old script that is really special-purpose, finding the surface area that is more red than blue after coloring by electrostatic potential. Note that this would include surface that looks white but has a tiny, tiny tint of pinkishness. Also, the surface area that is more blue than red is just the complement of the surface that is more red than blue. In other words, if the surface is 75% red>blue then it is 25% blue>red because very little if any will be pure white. They always add up to the total surface. So no, you cannot use these scripts to figure out how much of the surface is polar or nonpolar. It may not matter given the above, but which method, set of charges, and what parameter values to use for electrostatic potential (ESP) calculations are research decisions that I cannot make for you. There are always tradeoffs, and different people have different opinions, etc. I don’t know python, but your generalization to coloring by hydrophobicity by identifying cornflower blue vs.goldenrod might be wrong. Red vs. blue is simpler since they are RGB color components. However, even if the color comparison is done correctly, the logical problem is the same, they always add up to the whole surface, and nearly white areas will always be combined with one side or the other. However, you can get the total surface area given some range of hydrophobicity values independent of any coloring. Hydrophobicity in this case is just a constant lookup value for each type of amino acid, according to this table (kdHydrophobicity column): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> You would have to decide yourself which range of values is polar or nonpolar, but then you could just select all the residues that are less than or more than a certain value, e.g. command: select :/kdHydrophobicity>0.0 Alternatively you could just use command: select polar select ~polar …but you might not agree with what amino acids are considered polar, as shown in a table in this page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/resprop/resprop.h…> Then if surface is shown you could add up the area for the selected residues, e.g. menu: Tools… Structure Analysis… Attribute Calculator, and in that tool calculate attribute named whatever you want for “molecules” with Formula: sum(areaSAS.residue) (… or SES instead of SAS, to be compared with the corresponding total area given in the Reply Log when you show the surface) with option to “Restrict formula domain to current selection” and “Show calculation results in Reply Log" turned on, other options turned off, click Apply. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calcul…> Totally separate and not related to Chimera, but I happen to know of this web server you might be interested in, for comparing ESP of related proteins: <https://pipsa.h-its.org/pipsa/> Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 11, 2019, at 2:16 PM, Fernando Villa <fer.vdl1928(a)gmail.com> wrote: > > > Dear Elaine C. Meng, Ph.D > > I have some questions about electrostatic potential molecular surfaces and protein comparison. > > 1. The following scripts are added, edited from the redarea.py script of link http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts, considering that the script allows reading the surface in Å2 colored more red than blue area. > > 1. Add scripts: > > Command: > > > open > > -blue_area_03.py > > -cornflowerblue_area_03.py > > -goldenrod_area_02.py > > -red_area_02.py > > (the scripts are attached) > > > 2. I used the following commands: > > > open 4MZ2 > > > delete solvent > > > addh > > > addcharge > > > Surface > > coulombic -10 red 0 white 10 blue > > > The electrostatic potential surface is presented by Coulombing coloring Surface: > > > > <image.png> > I execute the commands: > > > redarea #0 > > red area 3562, total area 5730, ratio 0.6217 > > > bluearea #0 > > blue area 2168, total area 5730, ratio 0.3783 > > > The dominant areas of both colors are obtained. > > The following command is input: > > > rangecolor kdHydrophobicity min cornflowerblue 0 white max goldenrod > > > > <image.png> > Next: > > > cornflowerbluearea # 0 > > cornflowerblue area 4109, total area 5730, ratio 0.7171 > > > > goldenrodarea # 0 > > Goldenrod area 1621, total area 5730, ratio 0.2829 > > > So, I believe (I'm not sure): > > Blue area + Red area = PSA ß Is correct? > > White area = NPSA ß Is correct? > > > So, the real blue and red areas would be (not sure): > > > (Redarea * PSA) / Total surf = Real Red area > > (Bluearea * PSA) / Total surf = Real Blue area > > So: > > Bluearea = 1554.6792 > > Redarea = 2554.3208 > > > Is this calculation correct? > > > Could I apply these calculations to compare them with other proteins of the same family? > > For example: > > Protein members of the immunoglobulin family. > > > > In the Chimera version 1.14, I Download the following programs pdb2pqr-windows-bin64-2.1.1 > > apbs1.5_win64 > > Downloaded from the website: http://www.poissonboltzmann.org > > Next, I assign charges and radii with the following parameters of PDB2PQR > > > <image.png> > And I saved the file. Pqr > > > <image.png> > Later I opened the file 001_B4.pqr with Chimera 1.14 > > > <image.png> > I use the following command: > > > surface > > And run the APBS interface with the following default parameters: > > <image.png> > > As a result, the color gradient of the molecular surface appeared as shown: > > > <image.png> > <image.png> > > > However, my question is: > > Are these parameters correct using the force field PARSE of PDB2PQR? Or, is it necessary to use a different force field? > > > Could I apply the scripts: > > -blue_area_03.py > > -cornflowerblue_area_03.py > > -goldenrod_area_02.py > > -red_area_02.py > > > to calculate the redarea and bluearea and compare it with other proteins? > > > Is there a script that gives me the correct areas of both red and blue colors? > > > Sorry for my long email, as I am new to this area. And I really need help. > > I apologize for so many questions. > > I would greatly appreciate your help. > > > Best regards, > > Fer. > > > > > <blue_area_03.py><red_area_02.py><goldenrod_area_02.py><cornflowerblue_area_03.py>

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How to analyze cryo-EM reconstruction map of virus and prepare publishable figures?
by sunyeping 11 Sep '19

11 Sep '19

Dear all, I am new to cryo-EM structural biology. Now I have a cryo-EM reconstruction map for a virus particle. I wish to analyze the characteristics of the virus, such as the h, k and t number, the component of an cryo-EM asymmetric unit of the capid and prepare some publishable figures. I have no idea how to do these things. Could all these be done with Chimera? Is there any tutorials or manual for these calculation, visualization and drawing? If you could recommend some ways by which I can learn to do these, I would be greatly grateful. Best regards

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APBS electrostatic potential map not visible
by Ahmad Khalifa 10 Sep '19

10 Sep '19

Hello, After PDB2PQR and APBS calculation, I get an .dx that I can't view (doesn't appear when I click show), let alone color. I tried to launch volume viewer, it does display a surface. What am I doing wrong? Regards.

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Modeller from a Python script
by Samo Lešnik 10 Sep '19

10 Sep '19

Dear Madam/Sir, I would like to run the Modeller missing loop function implemented in Chimera by using a Python script, as I want to go through a number of protein structures. Is this possible? I do not find the appropriate commands in the comand list. I would use a local instalation of Modeller. Thank you for your help. Best regards, Samo

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DNA drawing inquiry
by Woorim Choi 09 Sep '19

09 Sep '19

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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.

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cage builder
by Artur Biela 06 Sep '19

06 Sep '19

Hi all, I would like to build a cage model using cage builder, but the problem is that I need to use different polygons than available in the pop-up window of cage builder. My question is: is there any option to use for example octagons, decagons or even more-gons? Thank in advance Artur =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Artur BIELA, PhD Scientific Assistant Bionanoscience and Biochemistry Laboratory Malopolska Centre of Biotechnology Jagiellonian University 7A, Gronostajowa Street 30-387 Krakow Poland Department of Cell Biology and Imaging Institute of Zoology and Biomedical Research Jagiellonian University Gronostajowa 9 30-387 Krakow artur.biela(a)uj.edu.pl http://www.mcb.uj.edu.pl/en_GB/heddle-laboratory publons<https://publons.com/mashlets?el=badgeCont570&rid=M-3954-2019> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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How could I know the segment label
by Huiya Zhou 03 Sep '19

03 Sep '19

Hi, I use the “Segment Map” for the volume data to divide the density map into parts. How could I know the information of each region? For example, the label, the average value of each region. I also would like to know the regions which are connected with one specific region. How could I obtain information in python script? Thanks, Huiya

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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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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 22 Aug '19

22 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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