July 2022 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] Assembling 2 proteins
by Elaine Meng 27 Jul '22

27 Jul '22

Hi Tata Santosh Rama Bhadra Rao, I already gave my suggestions in the previous message, so there is not really anything else I can do to teach you. Since you didn't give the details of all the steps that you tried and which step(s) gave results you didn't like, I can't tell you how to do it differently. My only idea is to go back to what I already suggested: you could use Matchmaker if you already had a pentamer, which you show in the bottom figures. So, following the instructions in my first reply, maybe you can take the chains shown in the top figures and match them onto the chains in the bottom figures to make the pentamer. However, that will only work if the proteins are very similar. If you did it already and it gave the bad result, maybe these proteins are not similar enough to use that approach. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 30, 2022, at 9:22 PM, SANTOSH RAMA BHADRA RAO TATA <19807877(a)students.latrobe.edu.au> wrote: > > Hi Elaine, > > I tried doing and it came out like this. Final 2 figures are homomeric pentamers. First 2 are heteromers with 3A subunits (A, B, D chains) and 2D (C, E chains) subunits. Could you please help me or teach me assembling them properly. > > Thanking you, > > With best wishes, > Tata Santosh Rama Bhadra Rao, > PhD Scholar, > C/O Prof Helen Irving, > La Trobe university, > Bendigo, Vic-3550, > Australia. > Email: 19807877(a)students.latrobe.edu.au; > S.Tata(a)latrobe.edu.au > Phone: 0499263974 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Wednesday, 25 May 2022 2:08 AM > To: SANTOSH RAMA BHADRA RAO TATA <19807877(a)students.latrobe.edu.au> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Assembling 2 proteins > > Hello Tata Santosh Rama Bhadra Rao, > It all depends on what information you have already. If you don't know how the pentamer is supposed to look (how the proteins fit together), then there may not be enough information: ChimeraX is not going to predict the pentamer structure for you. > > You said "5 different proteins" which I interpret to mean they are not 5 copies of the same thing, that it is a heteropentamer and not a homopentamer. If they were 5 copies of the same thing (homopentamer), then you might be able to use the "sym" command to build it from one copy, if the input file contains symmetry matrices in the header, or you know the symmetry and can specify it separately: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html> > > Otherwise: > You would only use Matchmaker if you also have an already-known structure of a similar pentamer. Then you would open the structure of that pentamer, open the structures of your five proteins (if the same one is multiple copies in the pentamer, you would open it multiple times), and then match each one of them to the similar subunit of the known pentamer. In other words, you would open 6 different PDB files and then use Matchmaker 5 times, once to match each of your proteins to the corresponding subunit of the pentamer. > > Just start Matchmaker (menu: Tools... Structure Comparison... Matchmaker) and in that dialog's Chain Pairing, choose "Specific chain(s) in reference structure with specific chain(s) in match structure". Choose one of your protein chains as the match structure and choose the corresponding chain in the known pentamer as the reference. Apply. Repeat with your second protein chain, etc. > > Here is the Matchmaker help with detailed explanations of all the options: > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#top> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > > On May 23, 2022, at 9:49 PM, SANTOSH RAMA BHADRA RAO TATA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hi, > > > > I would like to create a pentamer, how can I assemble 5 different proteins subunits into a pentamer. I was trying to use matchmaker but I couldn't. can you please help me with some video how to get in use it or if there is any other way to use the software and create pentamer please let me know. > > > > Thanking you, > > > > With best wishes, > > Tata Santosh Rama Bhadra Rao, > > PhD Scholar, > > C/O Prof Helen Irving, > > La Trobe university, > > Bendigo, Vic-3550, > > Australia. > > Email: 19807877(a)students.latrobe.edu.au; > > S.Tata(a)latrobe.edu.au > > Phone: 0499263974

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FitMap/FitList scripting
by Christian Tüting 27 Jul '22

27 Jul '22

Dear ChimeraX DevTeam, I am currently working on a project which requires fitting a single model multiple times in a map. This is easy doable with the global search parameter, and if n is big enough, all correct locations are found. My collegue Ioannis wrote you a couple of weeks ago to implement a copy function to the fitlist, but this includes only the statistics, but not the translation information of each model. This is only possible by clicking the button "Place Copy", which creates a copy of the model and applies the translation to this model. In the log, there is only the best model with the translation matrix, but if my map does have multiple correct locations, I'm missing this information. I extended the fitmap function in fitcmd.py, so it writes this to a file to the current location called fitmap.txt. This file contains all the statistics and the rotation/translation information. This might be handy for some users. Here is the code: f = open("fitmap.txt", "w") if len(flist) == 0: f.write("No fit found") else: for i, f0 in enumerate(flist): msg = f0.fit_message() f.write(f"Fit #{i+1}\n" + msg + "\n") f.close() Maybe you can include an option "to_text" (which is false by default), to actually add this functionality. Best Christian

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renumber command is unknown
by Kwangjun Lee 27 Jul '22

27 Jul '22

Hello, I am a new user of ChimeraX. I have tried to renumber AA but renumber is an unknown command. Is there any way that I renumber? For example, my current model starts C 1, I want to renumber it to C 20. Thanks for developing a great software.

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Fw: Cofactor Morph
by Colin Levy 27 Jul '22

27 Jul '22

Dr. Colin Levy c.levy(a)manchester.ac.uk Senior Technical Specialist (XRD) Manchester Institute of Biotechnology, Faculty of Science & Engineering Tel: +44 (0) 161 306 5168 The University of Manchester [cid:7fc572c6-1ad9-414b-9ab5-b520385d1c2d] ________________________________ From: Colin Levy Sent: 27 July 2022 12:58 To: chimerax-users(a)cgl.ucsf.edu Subject: Cofactor Morph Hello, I am new to Chimera X but looking to generate a morph between 4 states of my protein. The protein morph was very simple to achieve but I have been unable to figure out how to include the cofactor in my morph. The cofactor undergoes important rearrangements during the catalysis which I would like to capture in the movie. Thanks in advance, Colin Dr. Colin Levy c.levy(a)manchester.ac.uk Senior Technical Specialist (XRD) Manchester Institute of Biotechnology, Faculty of Science & Engineering Tel: +44 (0) 161 306 5168 The University of Manchester [cid:736ce72a-e048-40a9-88c8-978c7e7ced3b]

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movie recording while changing threshold level
by Elaine Meng 26 Jul '22

26 Jul '22

Hi Dmitry, You could do it using "perframe" with an embedded "volume level" command in your movie script. For example, the following gradually changes map #2 contour level from 2.5 to 0.5 over 50 image update frames: perframe "volume #2 level $1" range 2.5,0.5 frames 50 See the "perframe" help for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > > From: Dmitry Semchonok <semchonok(a)gmail.com> > Date: July 26, 2022 at 8:17:36 AM PDT > > Thank you very much for your tips. > Works as a charm. > How 1 more question if you please - > Is it possible to record a movie while your 3D map constantly changing its threshold volume level (from low to high - which is possible to set) ? > If yes, how? > Thank you in advance. > Sincerely, > Dmitry > >> >> Although it would still be nice to have a separate option, currently >> ndependent rotation can be scripted by using separate turn (or roll) >> commands as in this example from Tom Goddard: >> >> You can use the "model" and "center" options of the turn command to rotate >> each model about their own center. For example, rotating 2 models in 1 >> degree steps around the y axis for a total of 360 degrees >> >> movie record >> turn y 1 360 model #1 center #1 >> turn y 1 360 model #2 center #2 >> wait 360 >> movie encode side-by-side-spin.mp4 >> >> In this example the two models rotate at the same time. The turn command >> like other commands that create a motion returns immediately before any >> motion is done to allow you to start simultaneous motions. Then you use >> the "wait 360" command to wait until 360 frames have been rendered, then >> the .mp4 movie file is made. >>

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Adding H atoms
by Daniel VillanuevaAvalos 25 Jul '22

25 Jul '22

Hello, I am adding hydrogen atoms by entering addh#1 to the command line, and it works but when I export the pdb and import it into houdini, things are messed up. Sometimes it just doesn't show up and other times, just part of the structure shows up. Am I missing something? Thank you, Daniel.

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Re: [chimerax-users] Colab Modelled, but no PDB
by Tom Goddard 25 Jul '22

25 Jul '22

Hi Anthony, Predicting a dimer where the monomer is 1182 residues, so a total of 2364 residues is guaranteed to run out of memory on Colab or Colab Pro -- the GPUs they offer don't have enough memory (at most 16 GB). The web page on AlphaFold performance test cases shows that only an Nvidia A40 with 48 Gbytes of memory handles over 2100 residues. That web page gives results for running AlphaFold via ChimeraX on Colab, but also running AlphaFold installed on our machines at UCSF with either an A40 GPU or an RTX 3090 GPU (24 GB memory). The "no templates" means structure templates were not used when running on our UCSF machines. Tom > On Jul 24, 2022, at 1:35 AM, Anthony Morgan <anthony.morgan(a)pharm.ox.ac.uk> wrote: > > Dear Tom, > > Thanks so very much, this is low-hanging fruit for you, but invaluable for me as I am a newbie. Really appreciate it. The Test link is really illuminating too thank you. > > I had wanted to try a dimer of 1182 residues each, but I am doubting that this is going to work, even with the paid service. Agreed? > On the test page, one of the runs is annotated as “no templates”. I cannot see how you can add templates to the Alphafold panel. I only see Energy Minimization under Options. Am I missing something? > > I’ve now got the pdb of the one model, thank you. It’s obvious once it’s pointed out, but I couldn’t see the wood for the trees. > > Really appreciate your time. > > Kind regards, > > Anthony > > >> On 24 Jul 2022, at 00:37, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Anthony, >> >> AlphaFold predictions on Google Colab of 1200 amino acids often fail as you can see from test cases on this web page >> >> https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html> >> >> With free Google Colab you often get a very old Nvidia K80 GPU with 12 Gbytes of memory. With Colab Pro ($10/month) I usually get an Nvidia P100 GPU with 16 Gbytes of memory which can handle slightly bigger proteins. You can check what GPU you got by pressing the "+ Code" button on the Google Colab window, then entering the command "!nvidia-smi" and pressing the play button, which gives output like this >> >> Sat Jul >> 23 23:28:55 2022 +-----------------------------------------------------------------------------+ | NVIDIA-SMI 460.32.03 Driver Version: 460.32.03 CUDA Version: 11.2 | |-------------------------------+----------------------+----------------------+ | GPU Name >> Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |===============================+======================+======================| | 0 Tesla P100-PCIE... Off | 00000000:00:04.0 >> Off | 0 | | N/A 38C P0 34W / 250W | 16259MiB / 16280MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+----------------------+ >> >> >> To download a completed model after an AlphaFold error (typically out of memory), click on Files in the Google Colab window, then click on the predicted structure, "af1182_unrelaxed_model_1.pdb" in your image, and click the "..." to the right of the file and choose Download from the menu that appears. The file will then appear on your local computer in >> >> ~/Downloads/ChimeraX/AlphaFold/prediction_1 >> >> I'll see if I can add to the ChimeraX ColabFold output the GPU and also make it automatically download partial results in case an error occurs. >> >> Tom >> >> >>> On Jul 23, 2022, at 4:41 AM, Anthony Morgan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Dear All, >>> >>> I’m new to Chimera X and to Colab Alphafold (AF), hope you can help please. >>> >>> I’m running Chimera X 1.4 on a Macbook Air. >>> I want the predicted structure of a fairly large protein (1182 residues). >>> When I first ran Colabfold_predict, it terminated after 90 min (RAM issue). >>> I re-ran the same sequence *without * Energy Minimization. >>> After 20 mins, it successfully returned the first model (see attached), but ran into RAM issues again. >>> >>> Two questions: >>> >>> There is no ‘Prediction’ folder in my Downloads, so how can I download the *.pdb file of model #1 that it clearly has generated? >>> If I cannot do this, will an upgrade to Colab Pro solve this issue for this size of protein? >>> >>> Thanks for advice. >>> >>> Kind regards, >>> >>> Anthony >>> >>> <Screen Shot 2022-07-23 at 12.17.14.png> >>> >>> >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> >

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Movie recording
by Dmitry Semchonok 25 Jul '22

25 Jul '22

Dear colleagues, I have several maps and models that I would like to spin around independently at once and record as a movie. How to do that? Thank you in advance. Kind regards, Dmitry

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Question about commands similar to openModel in Chimera
by Thu Nguyen 25 Jul '22

25 Jul '22

Good morning, I am editing a python script that previously used the command chimera.openModels.list(modelTypes=[chimera.Molecule])to return a list of open molecules. Do we have a similar command in ChimeraX or is there any other way to get a list of protein chains in ChimeraX? Thank you very much. Best regards, Thu

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Colab Modelled, but no PDB
by Anthony Morgan 23 Jul '22

23 Jul '22

Dear All, I’m new to Chimera X and to Colab Alphafold (AF), hope you can help please. * I’m running Chimera X 1.4 on a Macbook Air. * I want the predicted structure of a fairly large protein (1182 residues). * When I first ran Colabfold_predict, it terminated after 90 min (RAM issue). * I re-ran the same sequence *without * Energy Minimization. * After 20 mins, it successfully returned the first model (see attached), but ran into RAM issues again. Two questions: * There is no ‘Prediction’ folder in my Downloads, so how can I download the *.pdb file of model #1 that it clearly has generated? * If I cannot do this, will an upgrade to Colab Pro solve this issue for this size of protein? Thanks for advice. Kind regards, Anthony [cid:8B6C8DAE-A4C3-4F95-8B26-037B6B318679]

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ChimeraX-users July 2022