September 2020 - Chimera-users - RBVI Mailing Lists

(no subject)
by Thirumurugan Prakasam 30 Oct '21

30 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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matchmaker and MSA
by arrafzaher＠campus.technion.ac.il 06 Oct '20

06 Oct '20

Hi, Suppose I have 3 structures #0 #1 and #2. If I impose structure alignment of both #1 and #2 to #0. I receive two MSA alignment. Is there a way to view one MSA of the 3 structures and not 2 MSA of them. Thanks, Zaher

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bound ligand's are exposed to solvent. Current calculations do not protect surface of ligand embedded in protein
by Anne-Frances Miller 01 Oct '20

01 Oct '20

Dear Chimera, I see on-line advice on calculating areaSAS and areaSES, however Chimera is calculating these for my bound flavin as if the protein were not there. I would like to assess the area exposed outside the protein, not total area (on an atom-by-atom basis). Indeed, the show surface command produces two surfaces, one for the FAD and a different one for the protein, even though both are chain A. Can I edit the pdb file to cause Chimera to create a single surface for both chains including both bound FADs, so that SASA calculated will represent the extent to which the FAD protrudes from the protein? (My protein is a heterodimer with two bound FADs, my Chimera version is 1.13.1 running on Mac OS 10.15.6) Thank you, Anne-Frances Novel Meritorious Research (and teaching) —————————————— A.-F. Miller, Ph. D. Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin Chair, Div. of Biological Chemistry, American Chemical Society

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Undo for volume eraser
by Ahmad Khalifa 30 Sep '20

30 Sep '20

Is there a way to undo a recent erasing that I did? Also, are there ways to use custom shapes, or other surfaces to erase density?

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scipy
by Hernando J Sosa 30 Sep '20

30 Sep '20

Is scipy installed with Chimera? If not how can it be installed? Thanks Hernando >From Chimera idle: >>> import chimera >>> import scipy Traceback (most recent call last): File "<pyshell#1>", line 2, in <module> ImportError: No module named scipy ___________________________________

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Re: [Chimera-users] Troubleshooting request for help
by Cain, Cheryl A 29 Sep '20

29 Sep '20

Hi Tanuja, I've added chimera-users(a)cgl.ucsf.edu to this email as they should be able to help you there. Thanks, Cheryl Cheryl Cain cheryl.cain(a)ucsf.edu Operations Coordinator, Department of Pharmaceutical Chemistry Accreditation Project Coordinator, School of Pharmacy UCSF ________________________________ From: Saswat, Tanuja (NIH/NCI) [F] <tanuja.saswat(a)nih.gov> Sent: Friday, September 25, 2020 9:56 AM To: chimera(a)cgl.ucsf.edu <chimera(a)cgl.ucsf.edu> Cc: Goins, Jerquan (NIH/NCI) [C] <jerquan.goins(a)nih.gov> Subject: Troubleshooting request for help Hi, I am a researcher at the NIH who uses this software to complete analysis. But as of recently some of the features that I usually use have not been able to access them. Can you guys assist me in finding a resolution. I’ve CC’s my IT support in case there was something above my cresds level. Regards -- Tanuja Saswat, Ph.D. Postdoctoral Research Fellow Laboratory of Dr. Laurie T. Krug HIV and AIDS Malignancy Branch (HAMB) Center for Cancer Research National Cancer Institute tanuja.saswat(a)nih.gov<mailto:tanuja.saswat@nih.gov> Building 10, Room 4A08 Ph:240-858-3201 NCI Website<https://urldefense.proofpoint.com/v2/url?u=https-3A__ccr.cancer.gov_HIV-2Da…>

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vop subtract removing too much of my map
by Ahmad Khalifa 29 Sep '20

29 Sep '20

I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1! how can I get precise subtraction?

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clustering models of a single pdb
by Subhrangshu Das 29 Sep '20

29 Sep '20

Dear sir, I have 100 pdb files. named as output.1.pdb to output.100.pdb what i do manually for clustering is as follows 1. select 100 pdbs -> open in chimera -> golto *File *-> *save PDB.. *-> *Save Multiple Models as PDB File *(renamed as all.pdb) 2. open chimera -> goto *Tools *->* MD/Ensemble Analysis *->* MD Movie* 3. in *Get Ensemble Info *dialogue box set -> *Trajectory format :* *PDB* *PDB frames contained in:* *single file* * Browse *to select File <all.pdb> *Use frames **first **through * *last* 4. on click *OK,* a dialogue box pops out, *MD Movie: PDB trajectory from all.pdb*, in which, goto *Analysis -> Cluster...*5.. on click* Cluster,* a dialogue box pops out,* Get Clustering Parameters,* in which I set *Cluster trajectory *as: *Starting frame: * *1* *step size: **1* *Ending frame:* * 100* *Cluster based on current selection, if any: * *true* *Ignore solvent and non metal ions: true* *Ignore hydrogens: * *true* *Ignore metal ions: * *alkali* 6. on click *OK, *after some RMSD calculation, i get the *Clustering* result, which I save to a text file <cluster> Now, as I need to do this for multiple times, I want to automate these steps by a python script. Can you please help with a scipt or some command help for the aforesaid tasks. Any help will be helpful in these regard. -- Thanks & Regards, Subhrangshu Das Junior Research Fellow, CSIR-IICB Department of Structural Biology & Bioinformatics Contact - IICB TRUE Campus, CN-6, Salt lake, Sector V, Kolkata-700091 *+919804938813*

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tile from command line
by Dieter Blaas 28 Sep '20

28 Sep '20

Hi, I am trying to use the command line command TILE as given here: Usage <https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/usageconvent…>: *tile* /models/ [ columns /N/ ] [ spacingFactor /f/ ] [ independentRotation true|false ] [ viewAll true|false ] [ label true|false ] I tried (following the syntax of e.g. "vol all level 0.02": "tile vol all columns 3" or "tile all columns 3" or "tile models all columns 3" or "tile #0, #1, #2, #4, #5, #6 columns 3" but none works can you please give me an example! 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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Is RTX support planned?
by Gokhan Tolun 25 Sep '20

25 Sep '20

Hi Tom, Are there any plans to implement RTX (real-time ray tracing) support to ChimeraX (and even better, allow the use of physically modelled materials and textures)? Thanks, Gökhan Gökhan Tolun<https://scholars.uow.edu.au/display/gokhan_tolun>, M.S., Ph.D. Senior Lecturer School of Chemistry and Molecular Bioscience<https://www.uow.edu.au/science-medicine-health/schools-entities/school-of-c…> | Faculty of Science, Medicine and Health (SMAH)<https://smah.uow.edu.au/index.html> | Room 125 / Building 18 Molecular Horizons Research Institute<https://www.uow.edu.au/molecular-horizons/index.html> Illawarra Health and Medical Research Institute<https://www.ihmri.org.au/researchers/gokhan-tolun/> University of Wollongong NSW 2522 Australia T +61 2 4221 3365 uow.edu.au<http://uow.edu.au/> | Facebook<https://www.facebook.com/UOW> | Twitter<https://twitter.com/uow> | Instagram<https://www.instagram.com/uow/> | LinkedIn<http://www.linkedin.com/edu/school?id=10255> NOTICE: This email is intended for the addressee name and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Please consider the environment before printing this email.

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Chimera-users September 2020