- Chimera-users - RBVI Mailing Lists

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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