December 2016 - Chimera-users - RBVI Mailing Lists

Hidden water molecules
by Michael Sharkey 11 Apr '19

11 Apr '19

Hi I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2). What am I missing? Thanks in advance Mike --

4 7

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

4 6

Mutation in Chimera
by Islam, Tanzila 06 Jan '17

06 Jan '17

Hi I am learning Chimera and I have gone through soe online tutorials. The tutorials showed how to introduce point mutation by Rotamers command. But it only allows to replace 1 ammino acid residue at a time. I want to insert 4-5 ammino acid residues in a gap of a sequence. Is there any standard procedure, command in Chimera that will let me do this type of residue insertion? This is really crucial for my research work. Thanks Tanzila Islam Graduate Student Washington State University

2 6

Showing color key programatically colouring from a volume...
by Pablo Conesa 31 Dec '16

31 Dec '16

Dear all We have this simple script to open a volume (#0) coloured using values from a second volume (#1): open betaGal.mrc open extra/MG_Chimera_resolution.vol volume #1 voxelSize 3.54 vol #1 hide scolor #0 volume #1 cmap rainbow reverseColors True For scolor command we are using a volume. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#volume It would be nice to achieve something like this at start up (note the color key is based on the volume): I've did it dragging the mouse over the canvas while "Color key" utility is open. And, is there a posibility to round up the values. Some kind of: Psaudocode: Give the resulting color key for each round values display the color key I guess that if there is a way to get the color key, then rest can be done through commands. Cheers, Pablo.

2 3

color zone on command line
by Kyle Morris 24 Dec '16

24 Dec '16

Hi Chimera dev, Following on from this post back from 2009: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003514.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003514.html> How would one also split map in this python script? Thanks! Kyle

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 164, Issue 26
by Healey, Joe 23 Dec '16

23 Dec '16

I might be able to offer a bit of help here, the Chimera team and Jaime helped me with basically this exact problem. I have a script here https://github.com/jrjhealey/bioinfo-tools/blob/master/strucfit.py that you could take from. You'll probably want to look specifically at lines 216-240. (Note - you'll also need to look at the relevant module imports for match and pychimera etc. The script will need Jaime's implementation of pychimera too (he's super helpful!) https://github.com/insilichem/pychimera The script gives output as below, as the script automatically finds the best matching PDB file (that's what the first 150 lines or so is looking for), there is additional information there. Best Model I'm Hit Comparing RMSD Assorted homology metrics 2k4r PAK_01796_model5.pdb 2.81843275676 37.5 13 0.00035 21.5 2k4r PAK_01796_model4.pdb 12.6869844869 37.5 13 0.00035 21.5 2k4r PAK_01796_model3.pdb 14.4133021316 37.5 13 0.00035 21.5 2k4r PAK_01796_model1.pdb 0.459177533295 37.5 13 0.00035 21.5 2k4r PAK_01796_model2.pdb 15.1861411912 37.5 13 0.00035 21.5 Hope that's useful! Happy to offer more help (though I'm sure the chimera team have it covered!) Joe M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738 ________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: 22 December 2016 20:00 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 164, Issue 26 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Saving Output From Match Align (Muk, Sanychen) ---------------------------------------------------------------------- Message: 1 Date: Thu, 22 Dec 2016 16:11:00 +0000 From: "Muk, Sanychen" <smuk(a)coh.org> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] Saving Output From Match Align Message-ID: <A69D81CB04F0734E96302AA9E36F9B233E521BEE(a)ppwexch2kx03.coh.org> Content-Type: text/plain; charset="iso-8859-1" Hello, I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays. Best, Sanychen Muk --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wi! sh to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) ---------------------------------------------------------------------

1 0

Saving Output From Match Align
by Muk, Sanychen 22 Dec '16

22 Dec '16

Hello, I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays. Best, Sanychen Muk --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) ---------------------------------------------------------------------

2 1

ChimeraX daily builds available!
by Elaine Meng 22 Dec '16

22 Dec '16

Prerelease daily builds of UCSF ChimeraX are now available to the public! UCSF ChimeraX home: http://www.rbvi.ucsf.edu/chimerax/ Download: http://www.rbvi.ucsf.edu/chimerax/download.html Please keep in mind that ChimeraX features are currently quite limited, that ChimeraX may not work on older machines and/or graphics cards, and that due to the upcoming holidays, responses may be slow if you contact us. On behalf of the Chimera/ChimeraX team, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

change default color maps
by Michał Kadlof 21 Dec '16

21 Dec '16

I found Palette Editor Tool, but I don't know how to use it. How can I apply chosen pallete in Surface Color Tool or load colors from palette into rainbow tool? -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

2 1

Crossfade and disp
by Daniel Asarnow 21 Dec '16

21 Dec '16

Hello Chimera experts, Here is another movie making question. I noticed that disp and ~disp trigger frames to be recorded, without a call to wait. For example: disp #2 movie crossfade 25 ~disp #2 disp #3 This would produce a movie that crossfades from model #2 to blank, with #3 suddenly appearing. To get crossfades between two ligands, I had to use: disp #2 movie crossfade 25 perframe "~disp #2" frames 1 disp #3 movie crossfade 25 Based on the documentation I wasn't sure if this was intended behavior or a bug. Did I miss a more elegant way to crossfade between two models? Thanks, -da

3 3