- Chimera-users - RBVI Mailing Lists

How to recreate point of view
by achatz 06 Aug '21

06 Aug '21

Hello, I have two Chimera sessions which originate from the same pdb. Through rotations and movements the sessions viewpoints diverged over time. Is there a way to synchronize one session with the other so it has the exact same viewing angle? Thanks Stefan

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Question about peptide connection
by Nicole Ostrovsky 27 Jul '21

27 Jul '21

Hello, I have a structure which I've cut a section out of and I am working on connecting the two loose ends together. I wanted to connect them with two glycine residues - since they are easiest to work with and have no side chains. I am doing this using the Modify Structure option under the Build structure tool and adding one atom at a time. However, when I try to minimize my newly created glycine, I get the error message "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached a picture of my reply log). I'm not sure how to troubleshoot this. Is there a better way to connect two ends of a peptide, or should I change the way I am using the modify structure tool? Thank you. Nicole Ostrovsky

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Changing DNA sequence
by Tom Goddard 26 Jul '21

26 Jul '21

Hi Gary, The swapna command lets you change a nucleic acid base, for example, to change residue 18 in chain C from a T to a G use open 1rsb swapna G :18.C Documentation for swapna https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/swapna.html <https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/swapna.html> Tom > On Jul 26, 2021, at 1:31 AM, <gren(a)lbl.gov> <gren(a)lbl.gov> wrote: > > Dear Tom > Thanks for many answers to our previous questions. > > I have one more question to our loved Chimera program. > > I have a NDA model (PDB), but the sequence is not right. Is there any way to use this DNA model to generate a new model with a right order of sequence? In other word, if is there an automatic/ simple method (by comment lines) to replace the sequence by the correct one in Chimera? > > Thanks a lot!! > Gary > > > Gang (Gary) Ren, PhD > Lawrence Berkeley National Laboratory > Molecular Foundry, Room: 2220 > 1 Cyclotron Road, MS 67R2206 > Berkeley CA 94720-8197 > Phone: (510) 495-2375; Fax: (510) 486-7268 > Email: gren(a)lbl.gov <mailto:gren@lbl.gov>; > https://rengroup.lbl.gov/ <https://rengroup.lbl.gov/>

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Query: Saved pdb doesnt have mutated residue
by ZUNERA JAMAL 26 Jul '21

26 Jul '21

Respected Chimera team! I have a pdb file in which i have done mutation by using swapaa command in IDLE python but once i saved the structure then new saved structure doesn't have mutated residues in it. commands: 1.rc("open filename.pdb") 2.rc("swapaa val #0:2.a") 3.new_file_name="val.pdb" 4.rc("write format pdb #0 C:\\Users\\folder" + new_file_name) 5.rc("save newsession") 6.rc("close session") 7.rc("close all")

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color pdb based on rmsd
by manikandank 21 Jul '21

21 Jul '21

Hi Chimera-users, I have aligned three pdbs using MatchMaker and would like to color one based on rmsd (per residue or per CA atoms). I see that i can use 'rmsd' to calculate CA-CA distance between two models, but i would like to write the distance difference in a file so that the file can be read in 'attribute' coloring scheme. Please let me know how to do this. thanking you with kind regards Mani.

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Doubts about DOCK6.9 and ZINC20
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 20 Jul '21

20 Jul '21

Hi, I’m a student and I’m currently doing a thesis. I’ve never used Dock or Chimera before, so I followed some tutorials but now I’m a bit confused. 1. For five months I’ve saved the prepared receptors and the ligands as mol2, but I didn’t choose “write current selection to @SETS section of file”. I’ve just read on Chimera that it “makes the currently selected atoms as a SET (as used to specify the rigid portion of a ligand in DOCK)”. The docking I’ve performed seemed to go, but is actually everything wrong because I didn't select the option? 2. I’ve generated the receptor without hydrogens after dockprep (so after assigning charges and hydrogens). I’ve deleted only hydrogens but maybe the charges are still there, is that an error? 3. I’ve always saved the receptor without hydrogens in mol2 instead of pdb, because I’ve seen this in some tutorials, but now I’ve read tutorials that save it in pdb. Is this another error? I was able to generate the surface even with mol2 no hydrogens receptor and I’ve always toggle on “use untrasformed coordinates”, but obviously the options to save the file change for mol2 and pdb. 4. I follow a tutorial online to download 3D molecules from ZINC20. Anodyne means there are no PAINS and no reactive groups? Is the most “clean” reactivity pattern? 5. I don’t know how to organize all the directories and subdirectories downloaded with ZINC. I downloaded them in format mol2 and method curl, is that correct or shoul I use fot the virtual screening another format and method? To perform a virtual screening, I need to save them in a single mol2 file? How can I do that without errors? I've seen the option "flat" in downloading method in ZINC, is this a way to download the molecules correctly for virtual screening? 6. I need to use Chimera, but even with ViewDock I’m not able to open so many molecules (190 822), how can I look at the results in the end? 7. I’ve saved the ligands’ mol2 files using sybyl-style hydrogen naming. Is that an error? 8. To perform the virtual screening using 3D molecules from the tranche browser of ZINC20, can I use them as they are or I need to edit them in some way (for example after downloading them, open them in Chimera and using add H and/or add charge)? I need very specific indications about all these questions, because I’ve never done something similar, it’s the very first time with all and I’m afraid of making mistakes. I apologize for the many questions, but I hope that someone can answer all my doubts. Thank you, Francesca.

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Help: Suitable graphic driver
by Nur Nadia Razali 20 Jul '21

20 Jul '21

Hi, I am Nadia, I am a newbie for Chimera UCSF. When I started using Chimera, fetch under uniprot search, the message popped up. [image: image.png] I really need you help regarding this. Is it the issue of graphic card? Could you suggest what is the suitable driver for me to buy. I do have this kind of problem with other software that requires me to have the driver. Thank you, Sincerely, Nadia *ChM. NUR NADIA BINTI RAZALI* Science Officer UKM Medical Molecular Biology Institute (UMBI) *p:* +603-91459187 *f:* +603-91717185 *w:* www.ukm.my/umbi *e:* nadiarazali(a)ukm.edu.my <azrulhisham(a)ukm.edu.my> *a:* Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, MALAYSIA. -- *PENAFIAN*: E-mel ini dan apa-apa fail yang dikepilkan bersamanya ("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat, rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Kebangsaan Malaysia (UKM) adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut. _*DISCLAIMER *: This e-mail and any files transmitted with it ("Message") is intended only for the use of the recipient(s) named above and may contain confidential information. You are hereby notified that the taking of any action in reliance upon, or any review, retransmission, dissemination, distribution, printing or copying of this Message or any part thereof by anyone other than the intended recipient(s) is strictly prohibited. If you have received this Message in error, you should delete this Message immediately and advise the sender by return e-mail. Opinions, conclusions and other information in this Message that do not relate to the official business of The National University of Malaysia (UKM) shall be understood as neither given nor endorsed by any of the aforementioned._

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Minimization troubleshooting
by Nicole Ostrovsky 19 Jul '21

19 Jul '21

Hello, I am trying to perform minimizations on some structures I'm examining and each time the minimization is done and I open the reply log, the gradient norm says "-nan" and it tells me that no atoms were updated. I wasn't able to find anything online about how to fix this, so I'm emailing to ask if anyone would know how to troubleshoot this. Thank you. Nicole Ostrovsky

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Blast protein webservice error
by Stefan Dobrev 14 Jul '21

14 Jul '21

Hello! I'm trying to run a homology model on a protein sequence using BLAST, but my Blast: query window shows up empty. At first I got this error in the reply log: File "C:\Program Files\Chimera 1.15\share\blastpdb\pdbinfo.py", line 151, in fetch_pdb_info import replyobj ImportError: No module named replyobj I solved it by changing the code to "from python import replyobj". Now I can actually see what the error is. A few more functions are called until we get to this: File "C:\Program Files\Chimera 1.15\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) error: [Errno 10054] An existing connection was forcibly closed by the remote host I've allowed chimera through the firewall and I have a modeller license key, I believe I've entered it somewhere in Chimera at some point. Any ideas what might be causing this? Thanks for any advice, Stefan Dobrev

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Flipping the map - resolution question
by Dmitry Semchonok 14 Jul '21

14 Jul '21

Dear colleagues, I heard that flipping the map in Chimera with the command vop zflip # will decrease the resolution of the map https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#notes <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#notes> Did I understand that statement correctly? If yes, how to flip the map without losing the quality (resolution)? Thank you Sincerely, Dmitry

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Running/opening issue of chimera on HPC login node
by Rajiv Ranjan Singh 14 Jul '21

14 Jul '21

I am trying to open/run chimer; installed on a cluster login node without root privilege. Installed in Home//.local/UCSF-Chimera64-1.15rc/ Getting the following error. *login1:*~/.local/UCSF-Chimera64-1.15rc/bin $ ./chimera libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 152 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 716 Current serial number in output stream: 717 Kindly advise me to rectify this issue. Best, Rajiv Ranjan Singh

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unable to open more than one map in Chimera
by Merk, Alan (NIH/NCI) [C] 12 Jul '21

12 Jul '21

Hello, I recently updated to Catalina on my Mac and I am now not able to open more than one file at a time in Chimera. Uninstalling the program and then installing the latest version from scratch did not fix the problem. Is there any way to resolve this issue? Alan

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Users group
by Zachary Morton 09 Jul '21

09 Jul '21

Hi, My name is zach morton, I am from UC Santa Cruz and I would like to be added to the user group please. Best, Zach

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WebGL file
by Avnam Ohri 06 Jul '21

06 Jul '21

Hello Chimera Team i have been trying to make a script for looping through a set of pdb files and get WebGL (.html) file as the output import os import chimera import Midas from chimera import exports from chimera import runCommand as rc # use 'rc' as shorthand for runCommand # change to folder with data files os.chdir("E:/files to work/") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: rc("open " + fn) rc("ac wb") rc("ac c2") htmlname = fn[:-3] +'.html' exports.doExportCommand("WebGL",htmlname) rc("close") This is the code I have been using in the script , but the output i get is not working , i have been getting 26kb files instead of 3-5 mb files and it doesn't show anything when I open it. can you please help me with the same as i am new to python code

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Volume subtraction of surface area between homology model and template
by Kovacs, Nicholas (CDC/DDID/NCIRD/ID) 06 Jul '21

06 Jul '21

Hello, I have a homology model that I have made and I would like to create a visual that portrays small surfaces where there is change in the solvent accessible surface area of the homology model compared to the template structure. I am trying to use the "subtract" map from map calculation which requires volume data for the 2 structures. I have tried the following to generate volume data and then subtract the volumes, but I am getting hundreds of small surfaces all throughout the area of the molecule: molmap #1 3 molmap #2 3 volume subtract #3 #4 I know molmap is likely not the command I want to be using since I am interested in the solvent accessible surface area but I have yet to find a command that will generate a volume corresponding to the volume enclosed by the solvent accessible surface area. I would greatly appreciate it if someone could help me find a way to create 2 volumes enclosed by the solvent accessible surface area of the 2 structures in addition to correctly configuring the "volume subtract" command to get my desired output. Thank you, Nick

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Webgl, python script for multiple pdbs
by Avnam Ohri 06 Jul '21

06 Jul '21

Hello Chimera Team i have been trying to make a script for looping through a set of pdb files and get WebGL (.html) file as the output. import os import chimera import Midas from chimera import exports from chimera import runCommand as rc # use 'rc' as shorthand for runCommand # change to folder with data files os.chdir("E:/files to work/") # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: rc("open " + fn) rc("ac wb") rc("ac c2") htmlname = fn[:-3] +'.html' exports.doExportCommand("WebGL",htmlname) rc("close") This is the code I have been using in the script , but the output i get is not working , i have been getting 26kb files instead of 3-5 mb files and it doesn't show anything when I open it. can you please help me with the same as i am new to python code

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Error in using chimera with structureviz2 and cytoscape
by SRUTHI NAMBIAR 30 Jun '21

30 Jun '21

Dear all, I have been using chimera for the past 1 year and recently wanted to club it along with the cytoscape software. But whenever I try to launch chimera through the structureviz app, I get the following message: Error message: Cannot run program "/home/students/chimera/": error=13, Permission denied I have changed the settings of structureviz to give the path of chimera which is /home/students/chimera. Still this error is occurring. Could someone help regarding the same? Thank you. Regards, Sruthi

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how to calculate RMSD
by Elaine Meng 30 Jun '21

30 Jun '21

> On Jun 30, 2021, at 7:19 AM, lufeiyu(a)jlu.edu.cn wrote: > > Dear Sir/Madam: > > I have a question about the analysing of the docking. I docked a peptide to the receptor using GALAXYpepDOCK. The results uncontained the scores of RMSD. Some literatures reorted the UCSF could calculate the RMSD. But I didn't get the way after reading the tutorials. Please help me to figure out how to obtain the RMSD of a docking structure .Thanks vwry much. Best wishes for you. > > sincerely yours > Feiyu Lu Dear Feiyu Lu, The chimera-users(a)cgl.ucsf.edu address is recommended for asking questions about how to use Chimera. I CC'd it here, so you do not need to send your question again. (Or if you are using ChimeraX, you should use chimerax-users(a)cgl.ucsf.edu in the future for asking questions.) An RMSD measures the difference between two different locations of a set of atoms. So in Chimera you would need to open not only the docking results, but also the position of that peptide that you want to use as reference to calculate their RMSD. Then, you can use the "rmsd" command to compare them. I cannot give an exact command since I don't know the model numbers you will have, but an example if you had the comparison peptide open as model #3 and the docking result models are #1.1, #1.2, #1.3 ... then your commands could be: rmsd #3 #1.1 rmsd #3 #1.2 [...] See rmsd command help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> The results would be shown in the Reply Log (open from Favorites menu). Also if you don't know what model numbers you have, look in the Model Panel (also can be opened from the Favorites menu). Model Panel help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Join models function on Chimera
by Azad, Roksana 29 Jun '21

29 Jun '21

Hi There, I hope you are doing very well. My name is Roksana Azad, I am a Ph.D. Student at the CUNY ASRC. I have been working on building a full length model of my protein into a cryoEM map, I have models for individual domain but not for the full lenght structure. I am trying to join the domain models using chimera "join models" function, but unfortunately it's not working for me. I tried everything I could find online about the issue, I used the addh command and kssdssp commands and also tried joining them using other bond instead of C-N, however my button for "apply" always grey and I can't click on it (please see the screenshot attached). I also tried this command "#0:127.A@C #1:1.A@N" according to my model # and atom, but its not selecting anything for me. I tried "combine" it also didn't work.? Please let me know if there is something else I am missing or what else I can do to create this bond or connection between two models. Thank you so much for your time and help in advance - very much appreciated. Sincerely, Roksana ________________________________ Roksana Azad<https://asrc.gc.cuny.edu/people/roksana-azad/> Ph.D. Candidate in Biochemistry & Biophysics Advisor: Kevin H. Gardner<https://kglab.ws.gc.cuny.edu/> Structural Biology Initiative; CUNY Advanced Science Research Center 85 St Nicholas Terrace * New York * NY * 10031 Phone: 212-413-3233 Email: razad(a)gc.cuny.edu

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Stuck in adding residue in the C-terminal of a segment
by Prathit Chatterjee 29 Jun '21

29 Jun '21

Dear Experts, This is regarding adding an ALA residue in the C-terminal of a specific protein domain, with CHIMERA. I have a protein-complex with multiple domains and chains. I want to add an ALA residue (101-th position) in the chain D, after the 100th residue which is PRO. I followed the tutorial and have given the following command in command line: addaa ala,101 :100.d The following outcome was: Couldn’t find ‘O’ backbone atom of PRO 100.D. Request you to kindly let me know what the possible solution could be, so that I add an ALA residue in the C-terminal of Chain D. Thank you in advance, Regards, Prathit Chatterjee

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how to know the net charge of my system
by Sara Luz Gomez Maya 29 Jun '21

29 Jun '21

Dear all, I'd like to know if there is a way to know the net charge of a system when opening the pdb file with Chimera. If so, is it possible to do it by means of the command line? Thanks in advance, Sara

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same chain id while saving large coordinate files
by manikandank 28 Jun '21

28 Jun '21

Hi Chimera-users, Chimera 1.15 (build 42258) puts same chain id for all protein chains present in the pdb during 'save pdb/write pdb' . I am using it in linux Ubuntu. Please help. thank you with kind regards Mani.

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Modeller..Waiting for the Opal server
by Hernando J Sosa 26 Jun '21

26 Jun '21

Dear Chimera, Today when trying to use Modeller through the Chimera interface (via web service) the program either stays forever in Waiting for the Opal server or produces a whole bunch of errors. Trying to run Modeller through the local installation also results in errors. Not sure if the problem is with Chimera or Modeller but one day ago Modeller&Chimera were working fine with the same input files that now are causing the errors (???). Thanks Best Hernando

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multi align viewer
by Jacqueline Vitali 25 Jun '21

25 Jun '21

Hi Elaine, When you do match-->align in chimera, you create the MAV. It has a coral region for the fully populated columns. If you change the order of the sequences, it automatically disappears. Is there a way to bring this region back? Thank you. Jackie Vitali Cleveland State University

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multialign viewer
by Jacqueline Vitali 24 Jun '21

24 Jun '21

Hi Elaine, When you do match-->align in chimera, you create the MAV. It has a coral region for the fully populated columns. If you change the order of the sequences, it automatically disappears. Is there a way to bring this region back? Thank you. Jackie Vitali Cleveland State University

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