August 2017 - Chimera-users - RBVI Mailing Lists

advanced option for WebGL?
by Albert 17 Aug '17

17 Aug '17

Hello, I noticed that Chimera can export a scene as HTML file which is based on WebGL. However, we can no longer change the displaying styles through this .html file since there is no any menu or option button in the page. Would it be good if Chimera could provide this function? As far as I know, PyMOL has similar function, but the generated .html provide a menu to change the scene styles. see here https://pymolwiki.org/index.php/Pymol2glmol Thank you very much. Albert

2 1

Draw Line
by Catherine Jenifer Rajam Rajendran 17 Aug '17

17 Aug '17

Hi Eric, Can you please tell me what are the ways to draw an axis. I have a directional vector - x, y, z coordinates (e.g., 0.407 -0.747 0.526) and a point (14.395, 37.07, -12.029). How to draw an axis in chimera tool with these two data? Thanks, Catherine

2 1

command line minimization
by Milo Westler 16 Aug '17

16 Aug '17

We are trying to automate the minimization of a series of compounds using the system command line. Since we have quite a few compounds, we are interested in using the Gasteiger method for assigning charges. The command line minimize includes the AM1-BCC method.. Is there a way to run an automatic minimization using the Gasteiger method? Currently we use: chimera --nogui --silent R.mol opt.cmd Where opt.cmd is: minimize write #0 R_min.pdb -- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center W. Milo Westler, Ph.D. NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo(a)nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ========

2 2

Match->Align commandline
by sonal rashmi 10 Aug '17

10 Aug '17

sir/mam, i want to use chimera Match->Align feature using the commandline or nogui script (python) to align multiple protein sequences (pdb files) to generate the alignment on MultiAlignViewer and save it as clustal (.aln) file. I tried out the python codes posted on the portals but non of them are giving proper alignment. kindly advice as to what i can do? Is there any commandline available for it? Thanking You Sincere User

2 1

Problem with added ions in Amber
by George Tzotzos 08 Aug '17

08 Aug '17

In MD movie I loaded complex.prmtop and complex.inpcrd files In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I’m attaching a snapshot showing the Na+ ions in red). I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 NOTE: I unticked the Removed existing ions/solvent box I obtained the following Warning “Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA I generated complex_solv.prmtop and complex_solv.inpcrd files When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below). > resinfo #Res Name First Last Natom #Orig #Mol 1 ASP 1 14 14 1 1 2 THR 15 28 14 2 1 ——————— 250 LEU 3988 4006 19 250 3 251 VAL 4007 4023 17 251 3 252 KBR 4024 4062 39 252 4 253 WAT 4063 4065 3 253 5 ———— 10272 WAT 34084 34086 3 10272 10024 10273 WAT 34087 34089 3 10273 10025 Is this what should be expected? Should I consider the solvated complex charge neutralised? Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions Thank you in advance for any suggestions.

2 3

chimera batch process
by y.turgay＠bioc.uzh.ch 08 Aug '17

08 Aug '17

Dear chimera users, I was wondering if you could help me automate the following procedure in order to batch process all my tomograms. What I want to do is to open a segmented tomogram, apply parameters like surface, the step size (1 of 8) to increase the connectivity of what has been segmented, to hide the dust (size: 50) and to threshold the tomogram to 0.5. Afterwards I would select all remaining objects and open a script to invert the surface and execute "mask #0 sel invert true" using the command line in chimera to substract the background from the tomogram. Finally I would save this as new map. Can anyone help me with the commands I have to write in the Terminal to iterate through 200 tomogram folder and automate and batch process this. Best Yagmur Turgay

2 1

looking for help in UCSF Chimera
by Ch Bilal 07 Aug '17

07 Aug '17

Respected Sir/Madam. Its Bilal here and i m doing research on a protein "rstA". I am UCSF Chimera user and i am facing an error while energy minimization i got a pop up windows with this error "No MMKT name of atom "HN1" in standard residue "LYS", please help me out i am attaching my complexes with this mail as well please find the attachment. Thank you!

2 1

Automatically changing rotamers
by Ali Malay 07 Aug '17

07 Aug '17

Dear all, I have a large, capsid-sized structure. Is there an easy way (e.g. using a script) to automatically change all of the rotamers of a particular residue type? For example, I would like to modify all cysteine residues such that they all correspond to the Dunbrack rotamer with Chi1= -61; could this be done using the swapaa command? Thank you in advance! Ali

2 1

surface calculation failed on new laptop
by Paul van Erp 03 Aug '17

03 Aug '17

Dear chimera users and developers, Recently I purchased a new laptop. One of the primary uses of this laptop is rendering structures using chimera and running VR simulations of these structures. I've used the new ChimeraX successfully for this. However I also use the old version of chimera for structure visualization, coloring according to attribute lists and I create morph models between structures. The new laptop is unable to calculate virtually any surface. I've gone through the various troubleshooting pages and tried many things. None seem to be effective. Is it possible that the surface calculation would be more successful on a different computer? Also would this depend on the hardware? or might a similar computer from a different brand suffice? Any help you could offer would be greatly appreciated. Thanks in advance, Regards, Paul van Erp

3 2

Volume transparancy
by Matzov Donna 02 Aug '17

02 Aug '17

Hello, I'm trying to make a movie such that a ribbon model would appear while its maps (represented as surface) is already shown and is partially transparent. For that I wanted to set the ribbon transparency to 100 and then use the following command: transparency 0,r frames 100 The problem is that when when the ribbon in 100% transparent, the shape is still apparent in the partially transparent map. the ribbon shapes are not seen only when the map is not transparent at all. Is there a way to fix that? Thanks, Donna

3 2

Chimera-users August 2017