- Chimera-users - RBVI Mailing Lists

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 17 Apr '20

17 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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