February 2018 - Chimera-users - RBVI Mailing Lists

Fw: Open MTZ file
by Williams, Joanne 20 Aug '20

20 Aug '20

Hello! Can you help with the inquiry below? thanks, Jo ________________________________ From: Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> Sent: Thursday, February 22, 2018 5:01 AM To: chimera(a)cgl.ucsf.edu Subject: Open MTZ file Is it possible to open an .mtz file in Chimera? ~~~~~~~~~~~~~~~~~~~~~~~~~~ Sharyn A. Endow, PhD Professor of Cell Biology, DUMC Professor of NBD, Duke-NUS PO Box 3709 450 Sands Bldg/Research Drive Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

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about select and label a residul with another different from the color of the whole model
by 张雷 13 Apr '19

13 Apr '19

Hi the experts of Chimera, Good noon! I had selected a residul and labeled it with the commands sel #0:500 rlabel #0:500. Then, the label can be displayed on the selected residul. How could I change the color of the label and display the label in a different color different from the color of the whole model? Thank a lot! Sincerely, Lei Zhang Peking University, Beijing, China

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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 --

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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

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Error in Windows saving a session
by Joel Mackay 21 Apr '18

21 Apr '18

Hi all Have other people seen (and solved!) this error before (below)? I'm having it crop up pretty much all the time now when I try to save a session (on my Win7 machine - running Chimera 1.11.2. Thanks Joel WindowsError Exception in Tk callback Function: <function command at 0x00000000155434A8> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save getattr(self, self.keepEquiv())() File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK self.Apply() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply self.command(1, self) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB saveSession(paths[0], **kw) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) WindowsError: [Error 32] The process cannot access the file because it is being used by another process WindowsError: [Error 32] The process cannot access the file because it is being used by another process File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) See reply log for Python traceback. ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay(a)sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/

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substituting atoms
by simon chapman 03 Apr '18

03 Apr '18

Hello...for my Master's dissertation, I need to substitute a sulphur atom for an oxygen in a Molecular Dynamics simulation. The run works fine with my target molecule 1KF1.pdb uploaded into Chimera, but the substituted version sends quite a few error messages and won't run. It doesn't appear to recognise the novel S atom. Any help would be much appreciated...I've been stuck on this for nearly a week! Best wishes Simon

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Density map segments and segment associated sequence extraction
by Ahmad Abdelzaher 26 Feb '18

26 Feb '18

Hello, I have a density map that i'm trying to segment. I want to fit in my structure in the segmented map, and save each segment of the map as an independent mrc map, and each corresponding segment of the sequence as a fasta file. How can I do that? Kind regards

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'Automatically' annotate multiple structures
by Healey, Joe 26 Feb '18

26 Feb '18

Hi again Chimera team, I'm looking for a fairly quick and dirty way to apply some annotations using 2D labels to a bunch of open structures. Basically, I have ~16 structures open on screen, which I then tile to compare. I'd like the model name to be displayed just below each model so that its easy to track. I've found this thread (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-July/004081.html) which appears to be attempting a similar thing (though I'd like to use the model.name not serial number), but the approach doesn't seem to work (no labels appear and there is no information in the reply log or IDLE to give me any clues). Any suggestions/alternatives appreciated! Joe Joe Healey 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

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Query
by priyanka bose 22 Feb '18

22 Feb '18

Respected Sir/Madam, I am a former research fellow and trying to use chimera for different view purpose. I tried for the mouse movement option but it is not working. Only some commands work in the downloaded software. Want to know, for the tools to be active is there any need of further license for the tools or any thing else. If yes is there any academic license facility and if no how could I rectify this problem. It will be helpful if I get to know where the problem is. Looking for your reply. Thanking you. -- Yours Sincerely, Priyanka Bose *Project fellow* *Dept. of Chemistry, BHU, Varanasi, UP* *M.Pharm* *Dept. of Pharmaceutical Sciences, Dr. H. S. Gour Central University, Sagar, MP* *Email: meow.bose(a)gmail.com <meow.bose(a)gmail.com>* *phone no: 8335828828*

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query regarding docking by chimera
by Juweria Shahrukh Effendi 21 Feb '18

21 Feb '18

Dear Daron I am new to chimera, I want to check the conserved water molecules in my protein pdb and its reported co-crystalized ligand as i do the dock prep complete adding hydrogen, applying charge, and i complete the whole steps the chimera isnt able to execute attaching the pic of both windows can you please have a look on it and guide me thanks With Regards Dr Juweria Shahrukh Effendi M.B:B.S, M.Phil Biochemistry, PhD Scholar (Computational Drug Design unit)Molecular Medicine Dr Panjwani Center for Molecular Medicine and Drug Research International Center for Chemical and Biological Sciences (ICCBS). Karachi Email i.d: javelightens@yahoo.com.http://sites.google.com/site/zaheerqasmi/groupmemberjavelightens83@gmail.com juweria.shahrukh(a)iccs.edu

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