April 2020 - Chimera-users - RBVI Mailing Lists

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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Chimera-users April 2020