November 2017 - Chimera-users - RBVI Mailing Lists

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

2 5

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

Error in Windows saving a session
by Joel Mackay 22 Apr '18

22 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/

3 7

Re: [Chimera-users] Analysis of the protein-protein binding interphaces in MARTINI models
by James Starlight 15 Feb '18

15 Feb '18

Thank you so much for the suggestions, Elaine! Indeed, I have turned off the both flags but the intra-models contacts are still recognized. it seems that in order to determine carefully the per-residual contacts between monomers, I should to make a backmapping of the CG models to AA. James 2017-11-27 9:23 GMT+01:00 <sdimicco(a)unisa.it>: > Grazie mille > > > Il 2017-11-23 04:47 James Starlight ha scritto: > > Thank you for the suggestions, Elaine ! > > I have already tried "Find Clashes/Contacts" plugin. In generally, it > works good, however its application on more complex oligomeric > patterns (e.g if I deal with 10-20 GPCRs in one system) is a bit > complicated. Briefly, if I select only one monomer and than try to > find its contacts with the rest of the atoms ( I have changed the > contact threshold to -1.2 for the MARTINI) - it works fine. However, > If I selected all of the atoms (even excluding inter-residue and > inter-molecular contacts) and changing the search criterium "against > themselves" - it found alot of contacts within the monomers. Does > anybody use any tricks for the MARTINI models to fascilitate the > contact searching? > > > James > > 2017-11-22 17:52 GMT+01:00 Elaine Meng <meng(a)cgl.ucsf.edu>: > > Dear James / Gleb, > This question seems too broad, perhaps. I don't know that much about > MARTINI, so I'm guessing instead of atoms you just have a bunch of points > that each represent multiple atoms. In that case you could probably use any > analysis that does not directly use exact atomic locations, atomic radii, or > atomic point charges. Analyses that DO use those things include > surface-area calculations, Find Clashes/Contacts, FindHBond. > > Maybe you should just first think about what Chimera analysis you want to > use, then just try it on your GC model and see if it works rather than > trying to get some exhaustive list of what might work. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Nov 22, 2017, at 2:23 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: > > Dear Chimera users! > > I would like to make some analysis of the protein-protein binding > established in coarse-grained MARTINI simulations. Briefly Chimera has > recognized a coarse-grained pdb file of 16 martini models of GPCRs. > What Chimera tools (e.g. contact maps, clustering of interphaces) > should work with CG models? What tricks should be used to make this > analysis easier? Because I am working with several proteins in one > system, I would like to work with its CG models without the conversion > to all atomistic representations. > > I thank you so much for the help! > James > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

6 15

Edition of the pdb/trajectories via Chimera
by James Starlight 04 Dec '17

04 Dec '17

Dear Chimera Users! I have a pdb file for the 16 monomers of the coarse-grained GPCRs and its corresponded trajectory in dcd. In both files all the monomers are defined as the same letter of the chain (X). My question: are there an easy way to assign a unique letter to each of the monomers in the both files via Chimera to facilitate the further analysis ? Thanks so much! James

2 4

Mutating to Lysine neutral
by Alireza Shaneh 30 Nov '17

30 Nov '17

Hello, I wanted to know if there would be a way to mutate the positively charged Lysine to Lysine neutral in Chimera. Thanks in advance, Alireza

2 1

hiding the structure elements
by chemocev marker 26 Nov '17

26 Nov '17

Hi Is there is way to hide all those structure elements which are not selected in chimera. best Jiri

2 1

Analysis of the protein-protein binding interphaces in MARTINI models
by James Starlight 26 Nov '17

26 Nov '17

Dear Chimera users! I would like to make some analysis of the protein-protein binding established in coarse-grained MARTINI simulations. Briefly Chimera has recognized a coarse-grained pdb file of 16 martini models of GPCRs. What Chimera tools (e.g. contact maps, clustering of interphaces) should work with CG models? What tricks should be used to make this analysis easier? Because I am working with several proteins in one system, I would like to work with its CG models without the conversion to all atomistic representations. I thank you so much for the help! James

2 3

Coulombic (Mailing list question)
by RYDER WHITTAKER HAWKINS 22 Nov '17

22 Nov '17

My Question of the Day: - I am running an MD movie in Chimera - I want to display the solvent excluded surface colored by coulombic potential. - I would like to implement this command as a script at each frame. What is the command? I am getting error after error... >coulombic -10 red 10 blue How could I put this in a Per-Frame analysis? Thanks for any suggestions. The documentation is not so clear for this coulombic function. Ryder Whittaker Hawkins MSc Candidate PI: Dr. Luc Vallières ryder.whittaker(a)crchudequebec.ulaval.ca ca.linkedin.com/in/ryderwh Work: (418) 525-4444 Cell: (613) 979-7729 Dept. of Molecular Medicine Université Laval (CHUL) 2705 Laurier Blvd Québec, QC G1V 4G2

3 9