September 2019 - 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 12 Sep '19

12 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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