- Chimera-users - RBVI Mailing Lists

Help!
by Kempfer, Jamie E. 31 Jan '17

31 Jan '17

i cannot get chimera to work on my windows computer!

3 2

Re: [Chimera-users] on chimera unit cell function
by Elaine Meng 31 Jan '17

31 Jan '17

Hi Smith, The Unit Cell results for a structure with and without “pack” are equivalent because the symmetry describes a repeating pattern: each single copy could be shown in any of several places around the first copy. In other words, as I said before, there are multiple equally correct ways of presenting the same information. Although I cannot spend a lot of time looking at your specific data, I see the 3 structures are all the same space group with similar unit cell dimensions and angles, and the paper says “we could present nucleotide-induced conformational changes in the same crystal lattice by eliminating possible artificial structural differences because of different crystal packing.” Therefore I infer that the crystal packing is approximately the same in the 3 structures. It cannot be EXACTLY the same, however, since there are conformational changes between the structures. Since I didn’t write the Unit Cell code or look at the symmetry matrices in detail, I don’t know why the structures don’t give the same arrangement without “pack,” but I don’t think it is important, since the different possible arrangements for a single structure are equally correct. I hope this helps, Elaine P.S. please send questions to chimera-users rather than to me individually - thanks > Begin forwarded message: > > From: "Smith Liu" <smith_liu123(a)163.com> > Subject: Fw:Re: [Chimera-users] on chimera unit cell function > Date: January 31, 2017 at 7:01:54 AM PST > To: meng(a)cgl.ucsf.edu > > Dear Elaine, > > Related to our previous communication on "on chimera unit cell function" , here I have more to discuss with you. > > Attached 1 was the paper “Nucleotide-Dependent Conformational Changes and > Assembly of the AAA ATPase SKD1/VPS4B” published in Traffic 2008. PDB ID 2ZAM, 2ZAN, 2ZAO were 3 pdbs from this paper, and 2ZAM was the VPS4B without any nucleotide, 2ZAN was the VPS4B bound with ATP, 2ZAO as the VPS4B bound with ADP. > > As the paper wrote, “Because our attempts to crystallize SKD1 (VPS4B) in the presence > of ATP or ADP failed, we soaked the apo form crystals in solutions of ATP or ADP”, thus the 2ZAN and 2ZAO were got by soaking the crystal for 2ZAM with ATP and ADP separately. All 3 crystals were with space group P 65. > > The pdb for the 6 mates for each of 2ZAM, 2ZAN and 2ZAO are attached in attachment 2, 3, 4 separately (prepared without clicking ""Pack molecules in unit cell"). If viewed by Chimera, you will find the mates of 2ZAM arrange in the same way as the mates of 2ZAO, i.e., the 6 mates connect each other closely (side by side) and packed in a screw way. However for the 6 mates of 2ZAN, although still in screw way, the 6 mates arrange not closely but have a space between the adjacent mates. Correspondingly, the diameters of the z-axis projection of the 6 mates of 2ZAM and 2ZAO were much smaller than that of the 6 mates of 2ZAN. > > However, if we by Chimera we click the "Pack molecules in unit cell",we will find the 6 mates of 2ZAN displayed exactly (or very similarly) as the 6 mates of 2ZAM and 2ZAO (Am I right). > > Then my question would be, in the crystal for 2ZAN and 2ZAO, do the proteins arranged in exactly the same pattern? And why if we did not click ""Pack molecules in unit cell", the mates of 2ZAN and 2ZAO were displayed differently, and with clicking ""Pack molecules in unit cell",the mates of 2ZAN and 2ZAO were displayed similarly? > > If the protein arranged differently in the crystal for 2ZAN and 2ZAO, then in the crystal packing of 2ZAN, how can I identify the 6 protein which were from the 6 screwed mates in 2ZAM? > > I am looking forward to getting a reply from you. > Smith > -------- Forwarding messages -------- > From: "Elaine Meng" <meng(a)cgl.ucsf.edu> > Date: 2017-01-30 04:05:22 > To: "Smith Liu" <smith_liu123(a)163.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] on chimera unit cell function > Hi Smith, > The number of copies and their positions are all correct no matter whether you choose the “pack” option or not. If you cut out a part of the real crystal, there will be a real copy in the same place as the copy from Chimera. So imagine if you had specified an infinite (or large) number of unit cells in Chimera, a chunk from the middle of the result would look the same as some chunk of the real idealized crystal, regardless of whether you used “pack”. However, since you are probably specifying 1 x 1 x 1 or some small number of unit cells, yes choose the “pack” option to show the copies packed together, instead of with some spaces where a copy is shown inside a neighboring box rather than in the central outline box. > Best, > Elaine > > > On Jan 29, 2017, at 5:10 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > > > Dear Elaine, > > > > I am still confusing on the function of "Pack molecules in unit cell" in Chimera. If we cut out a cube (or a volume) of crystal based on which a pdb was got, do you think the molecules packed in the cube in the way without "Pack molecules in unit cell" clicked, or the molecules packed in the cube in the way with "Pack molecules in unit cell" clicked? > > > > I am looking forward to getting a reply from you. > > > > Smith > > > > > > At 2017-01-29 00:50:44, "Elaine Meng" <meng(a)cgl.ucsf.edu> wrote: > > >Hi Smith, > > >It is my understanding that you will get the same number of copies whether or not you choose the “pack” option, and that there are multiple equally correct ways in which the copies will be positioned according to the symmetry information. The “pack” option simply chooses, out of these many equally correct alternatives, a configuration that places the centers of all the copies inside one unit cell outline box instead of spreading them out among neighboring boxes. > > >I hope this helps, > > >Elaine > > >----- > > >Elaine C. Meng, Ph.D. > > >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > >Department of Pharmaceutical Chemistry > > >University of California, San Francisco > > > > > >> On Jan 28, 2017, at 1:47 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > >> > > >> Dear All, > > >> > > >> In Chimera, we do Tools →Higher-Order Structure→Unit Cell, then what will be the diffenrence if we clicked "Pack molecules in unit cell" in comparison with if we did not click "Pack molecules in unit cell"? Does it mean that what we observed (or what Chimera displayed) if we click "Pack molecules in unit cell" , was really part of what it displayed if we did not click "Pack molecules in unit cell" but we increased the "Number of Cells" significantly? > > >> > > >> I am looking forward to getting a reply from you. > > >> > > >> Smith >

2 1

Save marker sets from command line or python
by Kyle Morris 30 Jan '17

30 Jan '17

Dear Chimera dev and community, I would like to save a marker set from the command line and ultimately do so in a script. Using the write command which I would use for PDB's, marker sets get saved in PDB format, of course. Is there a command to save the marker set as XML .cmm as it would from the volume tracer menu? I notice at the bottom of the following page this is a suggested development: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/… - supply Python code for reading and writing the XML files containing saved marker sets Is it there already and I can't find perhaps? Thanks for your help as ever! Best wishes, Kyle

3 2

on chimera unit cell function
by Smith Liu 29 Jan '17

29 Jan '17

Dear All, In Chimera, we do Tools →Higher-Order Structure→Unit Cell, then what will be the diffenrence if we clicked "Pack molecules in unit cell" in comparison with if we did not click "Pack molecules in unit cell"? Does it mean that what we observed (or what Chimera displayed) if we click "Pack molecules in unit cell" , was really part of what it displayed if we did not click "Pack molecules in unit cell" but we increased the "Number of Cells" significantly? I am looking forward to getting a reply from you. Smith

2 3

Metal Geometry Analysis - per frame
by Ilkow, Veronica 27 Jan '17

27 Jan '17

Dear All, Is there a way I could include the metal geometry analysis as a per frame script for a MD movie? Ideally I would like to have an output file which lists the best geometry and essentially prints out the co-ordination table for two atom selections per frame. I am trying to figure out how to use the python or chimera per-frame commands to specifically select an atom and then print an output file. Any hints and suggestions on how to do this will be greatly appreciated. Thank you in advance for your help. -Veronica

2 1

Re: [Chimera-users] dipoles
by Tom Goddard 25 Jan '17

25 Jan '17

Hi Vatsala, To change the arrow thickness change the line of code in the dipole.py script bildString = ".arrow %g %g %g %g %g %g .1 .2 .9" The values at the end control the shape, the “.1” is the cylinder radius, the “.2” is the arrow tip cone radius, and the “.9” is the fraction of the arrow length taken by the cylinder. This is described in the Chimera BILD format documentation here https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> Tom > On Jan 25, 2017, at 10:02 AM, Sagar, Vatsala (NIH/NEI) [E] wrote: > > Hi Tom, > Do you know how to change the dipole vector thickness. I am using dipole.py program to calculate dipoles in Chimera, and it is giving me a very thin line. > Thanks a lot, I sincerely appreciate it, > Vatsala Sagar > > From: "Sagar, Vatsala (NIH/NEI) [F]" > Date: Friday, January 6, 2017 at 10:09 AM > To: Tom Goddard , "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" > Subject: Re: [Chimera-users] dipoles > > Hi Tom, > I am attaching the PQR files and raw PDB files of the crystal structure of human gamma D with two monomers rotated 90 degrees to one another. Please take a look at it and tell me what you think, > Thanks, > Vatsala > From: Tom Goddard > Date: Thursday, January 5, 2017 at 7:07 PM > To: "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" > Subject: Re: [Chimera-users] dipoles > > Hi Vatsala, > > I guess you are refering to the dipole.py script on the Chimera Python scripts web page: > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > > Yes it should give the same answer for a molecule and a copy of that molecule rotated by 90 degrees. Without have the structure and rotated PQR files I don’t know what is going wrong. > > Tom > > >> On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F] wrote: >> >> Hi, >> Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? >> Thanks, >> Vatsala Sagar >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

1 0

on Multiscale Models
by Smith Liu 23 Jan '17

23 Jan '17

Dear Al, In the "Mutiscale Models" Windows , will you please tell me what does it mean for the item "Range"? I am looking forward to getting a reply from you. Smith

2 1

Python script for reading volume values at atom positions
by Kyle Morris 19 Jan '17

19 Jan '17

Dear chimera dev and users, Can anyone confirm with the latest chimera version (i’m running v1.11.2 build 41376) if this python script for measuring map values at atoms works for them? The script was reported previously on the users list here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-May/001587.html For me I get a python import error: from VolumeViewer import Data_Region, full_region, Rendering_Options Thanks for your insight! Best wishes, Kyle

3 6

beta sheet to loop
by chemocev marker 19 Jan '17

19 Jan '17

Hi I am looking at some region of the protein in chimera and it looks like a loop but the from the procheck analysis it shows a beta-hair pin like structure. In the electron density, its shows a hydrogen bonding between the main chain atom. Why is this difference and how to overcome on it. best Jiri

2 1

forget last question
by A G Szabo 18 Jan '17

18 Jan '17

Forget the last question regarding visualizing nucleotides as balls and sticks. Figured it out. ags

1 0