July 2021 - Chimera-users - RBVI Mailing Lists

Question about save images
by Chang, Jufang 29 Apr '24

29 Apr '24

Hi, there, I used Chimera for a very short period of time. When I just started using Chimera I was able to save image by going to "file" and "save image" to save the image on the display window. For some reason, this stopped working. Now, after I did the same thing, the image I saved has complete blackness (attached). I wonder whether I might get be able to get help from you. I also tried using command line to save image. The result is the same. The exact procedure I used are: Go to "Presets", choose "publication 1" , then go to "File" and "save image" I used window system. Thank you J ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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(no subject)
by Thirumurugan Prakasam 29 Oct '21

29 Oct '21

Hi, I am trying to make metal coordination bond as a dotted line and also I need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues. Looking forward to hearing from you, Many thanks, Thiru [image: image.png] -- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358

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Problems with installing on a Windows 10 expedition Dell laptop
by Alice Chen 10 Aug '21

10 Aug '21

Hello, I'm on a Dell XPS 9500 laptop running Windows v. 10.0.2.1000. When my IT specialist tried to install it, it would run the install program but at the very end the install would fail. We were able to install the old non-X version of Chimera. Is there something we should/can do to check, settings-wise? Cheers-Alice Kitterman Alice Y Chen AY Chen Illustration and Design https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos www.aliceychen.com

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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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Chimera-users July 2021