- Chimera-users - RBVI Mailing Lists

Chimera Visualization Tool
by Ela Ka 24 Feb '21

24 Feb '21

Dear Madam/Sir, We are a group of researchers who try to prepare educational contents in different aspects of protein molecular modeling for the students. Access to these educational content is not free. We need to prepare some pictures of proteins, ligand-receptor interaction, etc. for the slides. Can we use the Chimera software (free version) to prepare some pictures for the slides? Though, we won't use the tool, itself, for those educational sessions. Thank you for your consideration Best Regards Elaheh Kashani-Amin PhD, Bioscience

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No mmcif module in ChimeraX 1.0?
by Yangqi Gu 23 Feb '21

23 Feb '21

Dear Chimera Developer, I am trying to use an external python script to run some calculations. I am using ChimeraX 1.0 and the script requires the import of mmcif module but apparently it is not installed in ChimeraX 1.0? How should I install this module? I also downloaded a newer version 1.1, but it is a precompiled version. Do I need to remove ChimeraX 1.0? Because the older version was installed in /usr/bin with an executable file, but for the newer version, I assume I need to add the path for the executables? I also need to run some ISODLE refinement with my gpu, will ChimeraX configure gpu automatically? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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volume position/placement question
by Chen Mu 23 Feb '21

23 Feb '21

Hi Dear List, I am new to Chimera and I have a question using the volume viewer: I have three volumes (reconstructions from different tomographic reconstruction algorithms) to compare. They are in the same size and structure as saved in the .mrc files. I will rotate one volume and adjust the volume viewer and view it. And I then will create an animation video by adding 'roll' in timeline. But the question is, how can I make sure that when I open the other volumes, all of them are in the same starting position/placement, in order to compare and each frame in the animation video to make it possible to compare, because they should start at exactly the same volume position/placement. How can I set up this placement of the volumes to be the same? Thanks very much in advance! Best, Chen

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On pdb structure match or align
by Smith Lee 23 Feb '21

23 Feb '21

Dear All, With chimera I open A.pdb abd B.pdb. A.pdb contains domain a and doain b, B.pdb contains domain b and domain c, which is to say, the 2 structures share a common domain b. Will you please tell me the chimera specific command to align or match the 2 structures based fully on the common domain b in each structure, without consideration of the domain a and domain c for calculation of the alignment? Best wishes, Smith

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on chimera mask
by Smith Lee 22 Feb '21

22 Feb '21

Dear All, When I use command "mask ones #0" to get the mask for #0 image and use the mask.mrc for further processing by other program, it says the mask.mrc got was not in the "cube volume" format. Will you please explain what is the "cube volume" format mrc, and is any way to convert the above mentioned 'non-cube volume" format mask.mrc to "cube volume" format mask.mrc? Best wishes, Smith

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Green bars in side view on new install
by Rochelin Dalangin 21 Feb '21

21 Feb '21

Hello, I installed Chimera 1.15 on a Windows 10 Pro laptop running i5-10300H and Intel UHD 630. When I try to open side view to clip the protein, I end up with green bars on the side view window (as shown). I've tried reinstalling to see if that fixes the issue, but it didn't work. Would you have any idea what's causing this? Thanks, Rochelin [image: image.png] -- ------------- Rochelin Dalangin Department of Chemistry 4-135 Centennial Centre for Interdisciplinary Science University of Alberta Edmonton, AB T6G 2G2

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saving several pdb files in one
by Dieter Blaas 18 Feb '21

18 Feb '21

Dear Elaine and all, I have a large number of aligned pdb files and want to mask a volume including density near all these atoms. Is there an easy way of doing so? Usually I would load map and pdb, position the pdb model accordingly, activate all atoms and use 'zone' to mask everything further away from all atoms than a given distance. But this seams to be difficult with more than 100 coordinate files, each containing about 1000 coorinates! I also tried to combine all coordinates in a single file omitting everything else but chimera tries desperately to find secondary structure elements, which is difficult with this mess.... Is there an easy way of doing so? Thanks, best, 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@meduniwien.ac.at ------------------------------------------------------------------------

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Installing chimerax linux
by Francesco Pietra 18 Feb '21

18 Feb '21

Hello I would like to change to chimerax, installing it on Debian (10 Buster) Regrettably, it has become practice to refer to ubuntu when .deb packages are concerned. I would appreciate being informed which u. version, if any, is suitable for Debian 10 thanks francesco pietra

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Hide (pseudo-)bond between neighboring residues
by Konstantin Richter 18 Feb '21

18 Feb '21

Dear Chimera Community, I currently experience some trouble hiding certain bonds that Chimera automatically displays. But first things first: I want to design a figure of the active site of two very similar protein structures (models #0 and #1; let's assume they are mutants of the same molecule differing in only a few amino acid residues). I therefore display the ribbon as well as certain residues of model #0. Additionally, I align #1 on #0 and display the same residues in #1, but without the ribbon. So, the side chains of #1 should end in the ribbon of #0 (which is basically identical to ribbon #1). Since Chimera automatically displays all atoms of the residues when the respective ribbon is hidden, I also hide C,O,N of #1 residues. Now this looks fine expect for one thing. Chimera creates long (pseudo?)bonds between the CA atoms of residues that follow one another in sequence, e.g. res 64 and 65. This very long 'bond' messes up my figure, and I haven't yet figured out how to delete or hide it. I already tried the ~bond #1:64-65@CA command, but this one hides ALL bonds in residue 64 (but not the one between 64-Ca and 65-Ca) and other variations of the atom specifier. Is something wrong with my atom specification, or is this command not suitable for what I want to do? I also tried the bonddisplay command without succes, since it deletes all bonds in one residue. In the end, I want the residues of #1 to contain all atoms except for C,N,O including bonds between all atoms, but not the elongated connection between Ca atoms. best regards Konstantin Richter -- P. Konstantin Richter - M.Sc. Biochemistry Department of Structure Analysis of Biopolymers - Institute of Bioanalytical Chemistry Center for Biotechnology and Biomedicine (BBZ) - Leipzig University Deutscher Platz 5 D-04103 Leipzig Tel.: +49 341 9731316

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Writing each rotamers to individual PDB file
by Chemmama, Ilan 17 Feb '21

17 Feb '21

Dear Developers, I am trying to write a PDB for each rotamer in Chimera. I run the command: `swapaa RES :RESNUM lib Dunbrack criteria manual` I get the enumeration for each rotamers from SCRWL library. I was wondering if there was a way to write each of those rotamers into separate PDB file using a script. Some residues have large number of possible rotamers and manually selecting the rotamer and saving the PDB file is not tractable. Thank you very much ! Ilan

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fill solvent accessible channels
by Dieter Blaas 16 Feb '21

16 Feb '21

Hi, I am wondering whether chimera can fill/colour channels accessible from outside of a cryo-EM density map at a given level! If so, how? I'd like to check for size selectivity. Thanks, best, 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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Homology modelling with Chimera/Modeller
by StaidsonBio 16 Feb '21

16 Feb '21

Hi: I am trying to do homology modelling with Chimera/Modeler for a Fc fusion protein, which contains three domains, one is Fc, one is receptor and the 3rd is ligand. Fc has many PBD structures in PDB database and the receptor has couple of 3D structures with the ligand as well. I used the fusion protein sequence to do blast in Chimera and it gave matched sequence files to Fc domain only, no sequence files for the receptor-ligand complex, even it already has couple of solved 3D crystal structure files in PDB database. Is there any suggestion about this issue? Can I do separately, use Fc domain alone as search sequence for its template and use receptor-ligand sequences as search sequence for its template? If it is ok, there are two template files. How to make them into one template file for modelling late? Thanks very much for your suggestion. Sincerely TW Sent from Mail for Windows 10

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Cutoff for clustering
by Yasser Almeida 15 Feb '21

15 Feb '21

Hello, I have a question regarding the clustering in the MD Movie tool (MD Movie/Analysis/Cluster). What's the RMSD cutoff value to make the clustering? I don't see any mention of this in the documentation. Thanks in advance, -Yasser

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fitting open conformation (map)
by Neha Gandhi 13 Feb '21

13 Feb '21

Hi Elaine, There is a cryo-EM structure of the spike trimer in closed conformation. I have downloaded pdb file and map files for the locked conformation. I am interested in aligning or mapping map of the open conformation (fitting pdb from closed conformation pdb on the map). Could you please advise how this can be achieved? Many 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 <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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on chimera vop threshold
by Smith Lee 13 Feb '21

13 Feb '21

Dear All, I have a map (A.mrc). When I open it in chimera (the map should be #0), the Volume Viewer shows the Range is -0.618 to 1.63, the default Level is 0.175. With command "vop threshold #0 minimum 0.18 set 0" I got another map (let us call it B.mrc, should be #1), the Volume Viewer shows the Range is 0 to 1.63 (understandable, the maximum value is still 1.63 as in A.mrc, the minimum value is 0 as for all values not higher than 0.18 has been set to 0), the default Level is still 0.175. Immediately I run the command "vop threshold #1 maximum 0.17 set 1". Before I running the command, I guess all the density value should be either "0" or "1", because all the value lower than 0.18 has been set to "0", and all value higher than 0.17 has been set to "1". However after I run the command "vop threshold #1 maximum 0.17 set 1", I got another map (let us call it C.mrc, should be #2),the Volume Viewer shows the Range is 0 to 0.17 rather than 0 to 1, and wen I change the Level, the image of #2 changes correspondingly with the Level from 0 to 0.17. Here I would ask, why the command "vop threshold #1 maximum 0.17 set 1" did not lead to a map with all values greater than 0,17 as 1? How to get a map based on A.mrc so that all values less than 0.18 as 0 and all values greater than 0.17 as 1 (please tell me the specific method)? Is any significance for the obtained C.mrc with range from 0 to 0.17? I am looking forward to getting your reply. Smith

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Apple M1 chip
by 163 11 Feb '21

11 Feb '21

Hi There, Is there a version that is suitable for Apple M1 Mac? I found the old version is quite on M1 Mac. Thanks! ML

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Re: [Chimera-users] Creating new models from existing crystal structures
by Elaine Meng 08 Feb '21

08 Feb '21

You're welcome, I'm glad you figured it out! Elaine > On Feb 8, 2021, at 2:40 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > > Hi Elaine > Nevermind, I found my error. I tested the Join Model tool with 1AV1 which has four chains and I was able to correctly pick the correct C and N atoms to join residue segments from each chain. The select command that I had written originally wasn't right so it was picking the correct atoms to join. > Thanks for your help. > Best > Tiglath > > > On Feb 8, 2021, at 2:27 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > If the residue is already in a peptide bond, you can't add another peptide bond. You would have to delete the rest of the chain after 130 in one copy of the model and the rest of the chain before 131 in the other copy for it to make sense. > > > > Also, make sure that your "select" command is selecting exactly two atoms, 1 from each model. > > > > Elaine > > > >> On Feb 8, 2021, at 1:53 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > >> > >> Hi Elaine > >> > >> I've been using the biological assembly of 3R2P and I'm thinking that the reason why it's not working is because both chains are labeled A. I'm just following a paper where they're building a monomeric structure using the residue fragments but in their case the biological assembly of 3R2P is labeled as chain A and chain B. > >> From: Elaine Meng <meng(a)cgl.ucsf.edu> > >> Sent: Monday, February 8, 2021 1:01 PM > >> To: Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> > >> Cc: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> > >> Subject: Re: [Chimera-users] Creating new models from existing crystal structures > >> > >> Hi Tiglath, > >> If you just opened 3r2p one time, you only have one model. Join works on bonding two separate models. Also it contains only chain A (there is no chain B in this structure) and residue 130 in chain A is already bonded to residue 131 in chain A. So I do not understand what you already did to modify the structure(s) before joining, or what you are trying to do now, sorry. > >> > >> You could send a session file if you want. > >> Elaine > >> ----- > >> Elaine C. Meng, Ph.D. > >> UCSF Chimera(X) team > >> Department of Pharmaceutical Chemistry > >> University of California, San Francisco > >> > >>> On Feb 8, 2021, at 12:35 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > >>> > >>> Hi > >>> > >>> I'm trying to join two models together using the Build Structure tool but I'm having problems. Here is my process. > >>> > >>> • Using the 3R2P crystal structure I select residues 3-130 from chain A and 131-182 from chain B > >>> • Then using the following command in Chimera I select the N atom of residue 130 that will form a bond with the C atom of residue 131: sel #0:130@N#1:131@C (#0 is the name of the 3-130 segment and #1 is the name of the 131-182 segment) > >>> • Then using the Build Structure tool I select Form C-N peptide bond, but the Apply button doesn't activate. > >>> I don't understand what the issue is. Is the command that I've written wrong? > >>> > >>> I would be very glad for your help. I can provide the pdb files of the residue segments if necessary. > >>> Thanks > >>> > >>> Tiglath > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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Creating new models from existing crystal structures
by Moradkhan, Tiglath A 08 Feb '21

08 Feb '21

Hi I'm trying to join two models together using the Build Structure tool but I'm having problems. Here is my process. 1. Using the 3R2P crystal structure I select residues 3-130 from chain A and 131-182 from chain B 2. Then using the following command in Chimera I select the N atom of residue 130 that will form a bond with the C atom of residue 131: sel #0:130@N#1:131@C (#0 is the name of the 3-130 segment and #1 is the name of the 131-182 segment) 3. Then using the Build Structure tool I select Form C-N peptide bond, but the Apply button doesn't activate. I don't understand what the issue is. Is the command that I've written wrong? I would be very glad for your help. I can provide the pdb files of the residue segments if necessary. Thanks Tiglath

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Re: [Chimera-users] Video tutorials
by Tom Goddard 04 Feb '21

04 Feb '21

Hi Cynthia, Ok, I converted all the Chimera video tutorials (about 40 of them) to use standard web browser video playback. https://www.rbvi.ucsf.edu/chimera/videodoc/videodoc.html <https://www.rbvi.ucsf.edu/chimera/videodoc/videodoc.html> Thanks for pointing out that they were using the obsolete Flash plugin for movie playback. Tom > On Feb 4, 2021, at 10:29 AM, Cynthia Page wrote: > > Hi Tom, > Do you all have any plans of porting the tutorial flash videos to another player? I see there are some YouTube videos available for Chimera but I am thinking of the tutorials that are available on the website. > Maybe there is another source of video tutorial I am unaware of? > > Thanks very much, > Cynthia Page > CU Boulder > > Sent from my iPhone >

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MD simulation in Chimera : 10 ns simulation is equivalent to 1 million of production steps 10 fs each?
by Giovanni Roviello 29 Jan '21

29 Jan '21

Dear Sirs, I would like to perform a MD simulation by UCSF Chimera. Should I wish to perform a 10 ns simulation (for example) how could I set the parameters related to time? For example in production a number of phase steps of 1000000 and a time step of 10 fs is OK? Does the relaxation time Nosé thermostat has effect on the overall simulation time? In simpler words if I set 1000000 steps, 10 fs time step, and I leave selected Nosè thermostat with 0.2 ps (but leave unselected the barostat option) will it correspond to a 10 ns MD simulation? Of course if I will publish using Chimera I will cite the program and the reference as indicated in https://www.cgl.ucsf.edu/chimera/docs/credits.html Thank you in advance for your kind help. Kind regards, Giovanni _______________________________________________________ Dr. Giovanni N. Roviello, Ph.D. Researcher at Istituto di Biostrutture e Bioimmagini IBB - CNR; Via Mezzocannone 16; I-80134 Naples; Italy giroviel(a)unina.it giovanni.roviello(a)cnr.it http://www.ibb.cnr.it/?command=viewu&id=387&lang=en https://orcid.org/0000-0001-6065-2367

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less color depth possible?
by Cheng, Tat 27 Jan '21

27 Jan '21

Hi all, We are trying to set up cryoEM data processing in the university HPC. We use X2go for remote accessing the HPC, but it doesn't have enough color depth, so Chimera (24-bit) doesn't start. One workaround is to download the volume from HPC to local machine, but it is less convenient. But I wonder is there a way to use Chimera in less color? Thanks a lot. Best, Tat

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how to color an model by an attribute in chimerax
by sunyeping 27 Jan '21

27 Jan '21

Dear all, I wish to color an model by an attribute in chimerax. The attribute is the entropy which is calculted by an external software. I wrote the entropy values of each residue in a text file (attr.txt) like the following: attribute: entropy match mode: 1-to-1 recipient: residues :1 0.0 :2 0.0014948 :3 0.0090952 :4 0.0004805 :5 0.1102497 :6 0.0095258 :7 0.0008226 :8 0.0042205 :9 0.0037255 :10 0.0006678 :11 0.0027988 :12 0.0193925 :13 0.0153925 :14 0.0052115 :15 0.0020136 .......... However, when I input the command "color byattr attr.txt", I get the following error information: "No known/Registered attribute attr.txt" Could anyone tell me what is the correct way to do this? With many thanks. Best regards

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coloring the volume series
by Arto Pulk 26 Jan '21

26 Jan '21

Dear all, I would like to make a movie using volume series. I have 10 maps (from Relion) that I upload to volume series. Now I would like to color the moving parts of the map. One can use zone coloring, but it does not do the precise job to color specific volumes of the map as it is radius specific. Then there is "surface coloring" by "volume data value". I can make a mask and color the mask region, but it makes the color gradient and I do not have control of the region outside of the mask at it will be mixture of colors. The best way to color is to use "segment map" and then go to "Regions" and "color density map". It does good job to color specific map volumes but the colors are not permanent. If you Play the Volme Series then colors vanish. So, is there any good way to color Volume Series? Regards, Arto Institute of Technology University of Tartu Nooruse 1 50411, Tartu Estonia Dr. Arto Pulk email: arto.pulk(a)ut.ee phone: 58244846

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Chimera RMSD
by Elaine Meng 25 Jan '21

25 Jan '21

> From: "Sharyn Endow, Ph.D." <sharyn.endow(a)duke.edu> > Subject: Chimera RMSD > Date: January 23, 2021 at 11:27:17 AM PST > > Thank you for your work in developing Chimera. We are trying to use Chimera RMSD to quantitate twisting of a beta-sheet and would like to know what the syntax is to list rmsd values for specified residues corresponding to a beta-strand, not just for single residues. Is it possible to list these values using RMSD? If so, we would greatly appreciate knowing how to get started. > > Sincerely, > Sharyn Hi Sharyn, You can specify any sets of atoms/residues that you like in the RMSD command, as long as there are equal numbers of atoms in the two sets that you specify (from two different models). They will be paired in the order specified. We have a command-line "atom specification" syntax for that kind of thing. There is a longish page with lots of examples here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> In your case, you may need to specify residue numbers, chain ID, and possibly atom names if you just want to use alpha-carbons or backbone as opposed to all atoms of the residues. E.g. something like rmsd #0:12.A,57-63.A #1:14.A,59-65.A ... for all atoms of model 0 residues 12 and 57-63 in chain A vs. all atoms of model 1 residues 14 and 59-65 in chain A. Or to use CA-only or backbone only: rmsd #0:12.A,57-63.A@ca #1:14.A,59-65.A@ca rmsd #0:12.A,57-63.A@n,ca,c,o #1:14.A,59-65.A@n,ca,c,o Of course the numbers could be the same in the two models, I just was trying to give a more general example. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. the chimera-users(a)cgl.ucsf.edu address CC'd here is recommended for general Chimera how-to or is-it-possible types of questions

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adding chimera-trimmings alias
by Dmitry A. Semchonok 25 Jan '21

25 Jan '21

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