- Chimera-users - RBVI Mailing Lists

aligning proteins based on sequence alignment
by Neha Gandhi 23 Apr '20

23 Apr '20

Dear List, I know Chimera can provide sequence alignments based on structure superimposition (matchmaker). I want to superimpose proteins based on the sequence alignment.Is there a way to do this? Thanks, Neha -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate

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Re: [Chimera-users] Chimera-users Digest, Vol 204, Issue 20
by Oliver Clarke 22 Apr '20

22 Apr '20

Hi Dieter, Two things to try (alone or together): 1. Do a global search - first position your model in approximately the expected location, but without regard to orientation, and them something like: fitmap #1 #2 search 100 radius 5 (assuming #1 and #2 are model and map respectively). You should get a interactive table with candidate orientations, where hopefully there will be a clear separation between correct and incorrect solutions. Second - low pass filter the map. Fitmap will have a higher radius of convergence and be less prone to getting bogged down in local minima if you lowpass filter the map aggressively (10-15 Å is often a good place to start). Good luck! Cheers Oli > > ------------------------------ > > Message: 2 > Date: Wed, 22 Apr 2020 14:24:16 +0200 > From: Dieter Blaas <dieter.blaas(a)meduniwien.ac.at> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Fitting model into map > Message-ID: <31e708c3-e7c5-307f-706e-f0f0a7286c00(a)meduniwien.ac.at> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi, > > ??? I always spend many hours placing a pdb model into a density map of > a virus with Tools > Volume Data > Fit in Map. Usually I have to move > the model around to find a more or less good fit manually, otherwise > Chimera does not find anything. I also tried by first making a molmap > followed by something like 'fitmap #0 #1 resolution 4'. I am convinced > that there is a better way of doing this but so far I was unable to find > it. Can anybody please give me a quick hint! > > Thanks, Dieter > > ------------------------------------------------------------------------ > Dieter Blaas, > Max Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Mobile: 0043 699 1942 1659 > e-mail: dieter.blaas(a)meduniwien.ac.at > ------------------------------------------------------------------------ > > > > ------------------------------ > > Message: 3 > Date: Wed, 22 Apr 2020 09:31:29 -0400 > From: Greg Pintilie <gregdp(a)gmail.com> > To: Dieter Blaas <dieter.blaas(a)meduniwien.ac.at> > Cc: chimera-users <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Fitting model into map > Message-ID: <5973694D-6634-488B-B7FB-DF53ED796047(a)gmail.com> > Content-Type: text/plain; charset="us-ascii" > > > You could try Segment Map followed by Fit to Segments (both in the Tools -> Volume Data menu). More details and a tutorial here if needed: > https://cryoem.slac.stanford.edu/ncmi/resources/software/segger <https://cryoem.slac.stanford.edu/ncmi/resources/software/segger> > > Greg > >

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Picking from list?
by Martin Mielke 22 Apr '20

22 Apr '20

Dear all! I am new to Chimera so please accept my apologies in advance if this has been discussed previously. I have read in the documentation https://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html that Chimera features the "pick on screen" function. So far, so good. Now, I was wondering if there is also an equivalent for the "Control Panel" featured in the Swiss PDB-Viewer. It can be seen here: https://spdbv.vital-it.ch/main_guide.html It allows for a, maybe, more granular cheery-picking from a list. Selections can later be exported as PDB. Thanks in advance! Best regards, Martin

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Fitting model into map
by Dieter Blaas 22 Apr '20

22 Apr '20

Hi, I always spend many hours placing a pdb model into a density map of a virus with Tools > Volume Data > Fit in Map. Usually I have to move the model around to find a more or less good fit manually, otherwise Chimera does not find anything. I also tried by first making a molmap followed by something like 'fitmap #0 #1 resolution 4'. I am convinced that there is a better way of doing this but so far I was unable to find it. Can anybody please give me a quick hint! Thanks, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Change the formal charge of amino acid side chains
by Friederike Leßmöllmann 21 Apr '20

21 Apr '20

Dear Chimera users, I need to change the formal charges of all charged AA side chains in a protein to be neutral and all open valencies to be filled with explicid hydrogen. I am very new to Chimera and I basically downloaded it in hope to find a solution to my problem. I know, it is not common to change the charge of a side chain and shouldn't be done usually. Does anybody have an idea how to do this anyway? Thanks a lot in advance! With kind regards Friederike

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Accuracy of helical parameters
by Vadim Kotov 20 Apr '20

20 Apr '20

Dear mailing list, I have a question regarding command "measure symmetry" in helix mode. Is there a way to estimate the accuracy for the obtained helical twist and rise? My guess is that the accuracy is related to the pixel size, so if I have a map with a pixel size of 1 A, then the standard deviation for helical rise could be 0.5 A. Many thanks! Vadim Kotov Postdoctoral fellow, Löw lab EMBL Hamburg

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Re: [Chimera-users] Visualizing SARS-CoV-2 spike protein
by Chun-Nan Chen 20 Apr '20

20 Apr '20

Hello, I apologize. The PDB no. should be 6VSB. Thank you for your assistance. Chun-Nan Chen, Ph.D. CEO Single Cell Technology, Inc. 6280 San Ignacio Ave. Suite E San Jose, CA 95119 Mobile: (408) 642-9741 Email: chunnan.chen(a)singlecelltechnology.com <mailto:chunnan.chen@singlecelltechnology.com> Web: singlecelltechnology.com <http://www.singlecelltechnology.com/> From: Chun-Nan Chen <chunnan.chen(a)singlecelltechnology.com> Sent: Saturday, April 18, 2020 10:45 PM To: 'chimera-users(a)cgl.ucsf.edu' <chimera-users(a)cgl.ucsf.edu> Subject: Visualizing SARS-CoV-2 spike protein Hello, I am trying to visualize the SARS-CoV-2 spike protein, which is a trimer (PDB no. 6CRZ). I wish to surface chain B, which is in an "up" conformation) but it kept giving me an error message. I tried the "split" command and other solutions without success. I could surface just the B chain but I really want to surface all 3 chains and color the RBD. Could anyone help me with this issue? Thank you, Chun-Nan Chen, Ph.D. CEO Single Cell Technology, Inc. 6280 San Ignacio Ave. Suite E San Jose, CA 95119 Mobile: (408) 769-2171 Email: chunnan.chen(a)singlecelltechnology.com <mailto:chunnan.chen@singlecelltechnology.com> Web: singlecelltechnology.com <http://www.singlecelltechnology.com/>

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Visualizing SARS-CoV-2 spike protein
by Chun-Nan Chen 20 Apr '20

20 Apr '20

Hello, I am trying to visualize the SARS-CoV-2 spike protein, which is a trimer (PDB no. 6CRZ). I wish to surface chain B, which is in an "up" conformation) but it kept giving me an error message. I tried the "split" command and other solutions without success. I could surface just the B chain but I really want to surface all 3 chains and color the RBD. Could anyone help me with this issue? Thank you, Chun-Nan Chen, Ph.D. CEO Single Cell Technology, Inc. 6280 San Ignacio Ave. Suite E San Jose, CA 95119 Mobile: (408) 769-2171 Email: <mailto:chunnan.chen@singlecelltechnology.com> chunnan.chen(a)singlecelltechnology.com Web: <http://www.singlecelltechnology.com/> singlecelltechnology.com

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Using Transformation matrix in Chimera
by Chemmama, Ilan 16 Apr '20

16 Apr '20

Dear Developers, I have a set of maps that I am trying to transform the following way: i) Compute the transformation between a PDB and one of maps. This is trivial using fitmap command. ii) I would like to get the inverse transformation moving the PDB to its original position. I have tried to play with matrixget and matrixes but without much success in access the the inverse transformation. iii) Apply the inverse transformation to each of the map. I assume you can easily do that with move passing the inverse matrix obtained above with a little for loop on model #. iv) Save the rotated maps This is trivial using vop resample and volume save. As you may see, I am struggling with step 2. Is there an easy way to access that matrix, get the inverse, and apply to a set of models. I have tried to find a solution in both Chimera (using runCommand) and ChimeraX (using run from core.commands) but to no avail. Any tips would be appreciated here - Ilan

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Re: [Chimera-users] making microtubule+motor models
by Tom Goddard 16 Apr '20

16 Apr '20

Hi Cynthia, The description of making a microtubule model in an earlier Chimera post http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-October/011646.html was just applied helical symmetry to a tubulin dimer. It is a made-up model not based on fitting actual data. To do it right start with a microtubule electron microscopy map. Fit your tubulin, or kinesin or other motor atomic model into the map. Find the map symmetry (helical pitch, center, axis direction) and apply that symmetry to the atomic model. You might be able to get the map symmetry parameters with the Chimera "measure symmetry" command https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry Here is a tutorial making a ParM helical filament model. http://www.cgl.ucsf.edu/chimera/data/singapore-jul2012/parm.html <http://www.cgl.ucsf.edu/chimera/data/singapore-jul2012/parm.html> Send questions to chimera-users so others will be able to find the answers in the future. Tom > On Apr 16, 2020, at 10:06 AM, Cynthia Page wrote: > > Hi Tom, > > I have found your Chimera user group entry: How to make a microtubule model pretty helpful, thanks for posting this. I am especially naive with Chimera and would like to ask you assistance in making decorated microtubule models as reference maps or cryoem analysis. I can post our conversation to the Chimera group if you think it would be useful. > > I would like to make reference maps for The MiRP/Moors Lab procedure. MiRP interfaces with Relion to perform “helical" reconstruction of molecules bound to microtubules from cryo-em data. > > I have been playing around with you command > > sym #0 group h,9.8,27.7,13*shift,8,80.0 surf true axis x center 0,115,0 res 5 > > > While as you know it works fine with PBD ID 1jff, I cannot figure out how to get results from other PBD ID’s, those with Kinesin molecule and alpha/beta tubulin. I think the key is "axis x center 0,115,0” portion of this command, and the orientation of molecule as download from the PDB, but for the life of me I cannot figure out how to change the axis coordinates to orient the alph/beta/kinesin correctly. Can you tell me how to do this? I have been using PDB ID’s 3J8Y, and 2P4N. > > Thank you in advance for your time, > > Cynthia Page > Research Assistant > University of Colorado, Boulder > >

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vop subtract map minRMS
by Roberto Marabini 16 Apr '20

16 Apr '20

Hi, I have two questions regarding the command "vop subtract" with the option "minRMS". 1st question) In the help page the option minRMS is defined as: "the min RMS option can be used to scale othermap automatically to minimize the root-mean-square sum of the resulting (subtracted) values at grid points within the lowest contour of othermap." Does this mean that the value that appears in the "Volume viewer" window and labeled as "Level" is used to create a contour and all the grid pints inside this counter are used to compute the scale factor? 2nd question) If I understand the command, minRMS assume that the maps (let us called them V1 and V2) are related by a multiplicative factor. That is V1 = V2 * f where f is a scalar In my case V1 = V2 * f1 + f2 that is, both maps are related by a multiplicative factor (f1) plus and additive factor (f2). Is there any chimera command that compute the average of a volume so I can force both volume to have the same average? Thanks in advance. Roberto

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Enquiry regarding electrostatics calculations of outersurface
by Jian Chen 16 Apr '20

16 Apr '20

Dear all Chimera users, Chimera has capability to color molecular surface by electrostatic potential using data calculated by apbs module, and the values could be exported into txt files using the surfval.py script. However, there are too many electrostatic potential values exported, and the number of values seems exceed that of atoms. My question is, how to define a surface point whose electrostatic potential value whoud be calculated? I want to obatain the values of outersurface, how to screen out the values of outersurface of protein from them? I would greatly appreciate your help. Best Regards, Jian Chen

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Help with symmetry of fusion protein
by Hasan khan 15 Apr '20

15 Apr '20

Hi there I was hoping I could get some help with a modelling challenge that I am having as I am very new to protein modelling as a whole and Chimera. So I developed a fusion protein of a single monomer of an encapsulin structure (PDB:3DKT), I wanted to build the final icosahedral structure with the added fusion protein. So I tried to align 10 of the fusion monomers to the di-pentamer of the original PDB file and ran the sym command generating the native structure with the added fusion protein. I am unable to save this symmetry structure and I'm not sure if its due to the alignment of the 10 monomers onto the di-pentamer that I did first and then ran the sym command using coordinates of the original PDB or if Chimera is not able to produce coordinates for the structure in a new PDB. When I export it as a PDB the coordinates are not saved. So I was wondering if there is a way I could save this newly generated structure as other methods are not currently working. Thank you Kind regards HK

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remove of the list
by Jose Alirio Mendoza Mesa 15 Apr '20

15 Apr '20

Please, could you remove my email from the list. *Qco. JOSE ALIRIO MENDOZA MESA* Candidato a Doctor en ciencias Universidad Nacional de Colombia. cel. 3173829637

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Saving changes made in PDB files
by Liam fletcher 15 Apr '20

15 Apr '20

Good day, I am hoping you may be able to help me with an enquire I have for current work I am performing using the Chimera software for my final year project. I am attempting to save a PDB file separately following changes made e.g. Highlighted reside(s), change the background. I am having trouble in saving these files separately. More specifically, I am attempting to save different file versions where changes have been made to the protein for predicting the function. Is there a way to save these PDB files as I have been following the instruction. But, I am confusion about which of these instructions is the right instructions to use. I thank you in advance and hope to hear from you soon. Kind regards, Liam Fletcher

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CSG of a kind
by Esser, Lothar (NIH/NCI) [E] 14 Apr '20

14 Apr '20

Hi, I am sure this is possible I just could not find it in the documentation: Can someone quickly remind me how to subtract density that surrounds a molecule so as to leave the extra density in the map ? Volume eraser seems to use a sphere but this is too crude. I am interested in an extra domain that is not (yet) in my model and it would help to remove the portion that I know from the density. There is probably a very simple solution that I just can't seem to find. Thanks, Lothar

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Charge assignment to a ligand
by Prabuddha Bhattacharya 14 Apr '20

14 Apr '20

Dear Sir, I had a query regarding charge assignment to any ligand in chimera. While minimizing the energy of a particular ligand (Tools --> Structure Editing --> Minimize Structure) and also during Dock Prep, I found that for most of the aliphatic and alicyclic amines, they are getting protonated with a residual positive charge; while the aromatic amines remain unprotonated (and hence no residual charge). I understand that this is because of their differential pKb values (basic strengths). On the other side, deprotonation never occurs with the carboxylic acid (-COOH) group. Does the Chimera (force fields) control this issue of protonation and deprotonation considering the physiological pH ? I will be extremely grateful if some one may kindly clarify my doubts. Thanking you in advance, With Best Regards, *Dr. Prabuddha Bhattacharya * *Dept. Of Chemistry* *Adamas University* *Kolkata 700126* *India*

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Re: [Chimera-users] [chimera-dev] icosahedron with a T number
by Wei Zhang 11 Apr '20

11 Apr '20

Hi Elaine, I am able to use hkcage and build a spherical sphere with pentagons and hexagons. Is there a way to color those pentagons differently? Thank you, Wei On Fri, Apr 10, 2020 at 10:41 AM Wei Zhang <zhangwei(a)umn.edu> wrote: > Hi Elaine, > > Thank you for the quick reply and the instructions. > I will use the other email address next time. > > Best regards, > > Wei > > On Fri, Apr 10, 2020 at 10:12 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > >> Hi Wei, >> >> Take a look at the "hkcage" command if you want hexagons and pentagons >> instead of triangles. You give it the h and k values which are related to >> T number by the equation shown in that page: >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html> >> >> For this kind of question (next time) you probably want the >> chimera-users(a)cgl.ucsf.edu mailing list, not chimera-dev which is more >> for programming questions. >> >> Thank you for the good wishes -- you stay safe too! >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> > On Apr 9, 2020, at 4:21 PM, Wei Zhang <zhangwei(a)umn.edu> wrote: >> > >> > Hello, >> > >> > I have been playing with the icosahedron utility in Chimera. I really >> like this feature, especially with the sphere factor. >> > >> > The current routine uses a subdivision factor to represent the number >> of triangles on an icosahedral surface. However this lattice is not the >> same as we see in icosahedral viruses, which use a T number to designate >> symmetry. With a subdivision number, there are always hexamers on any edge >> of the icosahedron, whereas in the virus structure this is not the case. >> > >> > I am wondering if Chimera has an utility that can use the T number as >> the basis for building an icosahedron surface. >> > >> > Thank you. >> > >> > Hope everything is going well and stay safe! >> > >> > Wei >> >>

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MINIMIZATION BY CHIMERA
by Jonathan Javid 09 Apr '20

09 Apr '20

Dear Instructor Please guide meabout how minization is performed of protein Structure from chimera.Guide me step by step kindly. Waitig for your positive response. Thank you Reagrds Jonathan Javid

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How to to do that in chimera?
by Krivic, Denis 09 Apr '20

09 Apr '20

To whom it may concern, I have just started working on a project which includes docking and analysis of the results several weeks ago. So figuring out software for docking and the docking procedure itself was one set of problems (solved), and now I could really use your help in order to analyze my data - docking results (output files). At the moment, I am using Windows 10 (x64), Chimera 1.14, AutoDock Vina 1.1.2 and AutoDock 4.2.6. So, I have a protein (ion-channel) and several different ligands, for which I want to see how they and if they (at all) may interact with the protein. Therefore I dock the ligand in the two mentioned programs and got different output files. Vina generates a single file with 9 different positions, and 4.2. generates 9 different files for each position. Now, the first problem I encountered was that in Chimera I can open and analyze only Vina output (single file). How do I open 4.2. output? The second problem is that I am able (know how) to analyze polar interactions (HBonds). But can I somehow check for hydrophobic or other kind of interactions? The third thing is that, for example, I have Vina output files for ligand docked in 2 different (but adjacent) places in protein (so 18 positions in total). Is there any chance to merge those files so I can see the energy differences among all of them? Fourthly, is there any way to merge vina and an other program's output (4.2 or DOCK for example) and see if there are common structures (same one generated by both) and the ones that are not common for the two? Finally, is there any graphical way of representing the docking poses and see the likeliness of the binding of a certain poses? Or some sort of clustering of poses into more probable binding candidates or something similar? Thank you in advance, Denis What kind of docking What you want to do, meaning achive Which steps have you carried out Description of the status, when you get stuck

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How to split multiple ligands in mol2 files
by sunyeping 09 Apr '20

09 Apr '20

Dear all, I seem to read some posts in the chimera email-list that discuss split combined mol2 files contains many compound into single mol2 files for virtual screening, but now I cannot find them. I wish to do some virtual screening with autodock 4. I have split a sdf file contains over a thousand compounds into single mol2 file with the linux shell "csplit" command. However, I find lots of such mol2 files still contain multiple ligands （LIG1, LIG2, LIG3, etc.) whose coordinates mix together and so can not be split by shell command "csplit". Please find three such examples at: https://drive.google.com/drive/folders/1AiW00lbA4tRfLu-l47QfxWVn8PqnQ-5J?us… I can split the ligands in a mol2 file manually in Chimera GUI: first open the mol2 file, then select the ligands and save them as pdb files respectively to get separate pdb files for these ligands. After then reopen these pdb files respectively and save them as mol2 file. However, to process a large amount of mol2 files manually is impossible, so I need a command or script to do this. I hope chimera can do this. Chimera has a command "split": split [ model_number(s) ] [ chains ] [ ligands ] [ connected ] [ atoms atom-spec ]n However, it doesn't seem to be suitable for my scenario. Does anyone know whether chimera can split such mol2 files and how? I will appreciate any help of you. Best regards. Yeping Sun

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Issue: laptop gets sooooo hot when running chimera
by Yangfeng Li 06 Apr '20

06 Apr '20

Hi, I've been using chimera for several years. Recently I used it on my macbook air (2019 model, macOS 10.14) and found that it gets extremely hot when operating chimera even for ten minutes. That doesn't occur on windows laptops. So I guess the software might have some further optimization to better work on macOS. Hope to see a new version of Chimera launched soon. Stay safe and healthy, Loyal user Yangfeng

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2D diagram and CDK-Depiction.jar
by David Ricardo Figueroa Blanco 06 Apr '20

06 Apr '20

Hi! I am trying to generate 2d diagrams with Dockview from autodock vina outputs but I get this problem : Web Service: cdkdepiction converts either SMILES strings or MOL2 files into 2D structure diagrams in PNG format Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/CDKDepictionService Opal job URL: http://webservices.rbvi.ucsf.edu/appCDKDepictionService1586137005272-807576… CDKDepictionService stderr ----- Error: Unable to access jarfile /usr/local/cdk/CDK-Depiction.jar ----- CDKDepictionService stdout ----- [no output] ----- Structure diagram generation failed; see Reply Log for more information Any suggestion or needed program to install? Thank you !

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Download Chimera using CLI
by Reza Khayat 06 Apr '20

06 Apr '20

?Hi, Is it possible to download chimera headless using the command line interface? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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chimera session does not save new position of map
by Irina P. Suarez 06 Apr '20

06 Apr '20

Hi, I have a problem, for some reason my chimera session stopped saving the new position of my maps, meaning I open a few maps I align them and save the session, I close chimera and open the session again and the maps are again in their original position. Do you have an idea of what could the problem be? Also it does not let me save the session with “save session”, the option appears in gray in the file menu, it only allows me to do “save session as…”. Thanks for your help! Best, Irina

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