XYZ files

[vlad_gunko@…]

Dear Sir / Madam,
Many thanks for ChimeraX.
However, there are some problems on the use of some files.
(1) It will be better if ChimeraX could read files which can be read by Chimera (e.g., *.xyz).
(2) Some files produced by Chimera (e.g. *.PDB from *.xyz) are not read by ChimeraX.

Sincerely,
Vlad Gun'ko

[pett]

Hi Vlad,

Yes, ChimeraX cannot yet read every format that Chimera could. You are the first to request XYZ format, but I'm sure that others would want it too. Funnily enough, the ChimeraX Programmer's Manual tutorial uses as its example writing a plugin that reads XYZ files. So if you actually went through that tutorial you would wind up with a plugin that allowed you to read XYZ files. At any rate, I'm sure we'll directly add XYZ reading at some point in the not-too-distant future, and you'll be notified when that happens (since this ticket will then go to "fixed" status).
ChimeraX should be able to read PDB files based on XYZ structures. Can you provide an example file where this isn't working?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[vlad_gunko@…]

Hi Eric,
Now PDB files converted from XYZ using ChemOffice are OK (before I used another program). 
Files *.xyz and *.ml2 are not read.

Additionally, OpenGL 3.3 required could be higher than ones possible with old video cards (e.g. only OpenGL 3.1).

As a whole, a Linux version (on Fedora 32), x64.rpm, of ChimeraX 1.1 works better than 1.0 one on Windows 10.
Thus, you could add Fedora to RHEL/CentOS in your rpm list. 

Vlad

--- Исходное сообщение ---
От кого: "ChimeraX" <chimerax-bugs-admin@cgl.ucsf.edu>
Дата: 19 июня 2020, 20:00:22

#3422: XYZ files
-----------------------------------+----------------------------
          Reporter:  vlad_gunko@…  |      Owner:  Eric Pettersen
              Type:  defect        |     Status:  accepted
          Priority:  normal        |  Milestone:
         Component:  Input/Output  |    Version:
        Resolution:                |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  new => accepted
 * component:  Unassigned => Input/Output
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Eric Pettersen


Comment:

 Hi Vlad,
         Yes, ChimeraX cannot yet read every format that Chimera could.
 You are the first to request XYZ format, but I'm sure that others would
 want it too.  Funnily enough, the ChimeraX Programmer's Manual tutorial
 uses as its example writing a plugin that reads XYZ files.  So if you
 actually went through that tutorial you would wind up with a plugin that
 allowed you to read XYZ files.  At any rate, I'm sure we'll directly add
 XYZ reading at some point in the not-too-distant future, and you'll be
 notified when that happens (since this ticket will then go to "fixed"
 status).
         ChimeraX should be able to read PDB files based on XYZ structures.
 Can you provide an example file where this isn't working?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3422#comment:1>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

sio44n2.pdb​

part2.xyz​

sio88.ml2​

[vlad_gunko@…]

Added by email2trac

[vlad_gunko@…]

Added by email2trac

[vlad_gunko@…]

Added by email2trac

[pett]

Hi Vlad,
	I am going to break the problems you reported into separate tickets so that they can be assigned to different people and be closed individually as each problem is fixed.
	As for the OpenGL 3.3 requirement, that's what it is:  a requirement.  If we didn't need features only available in 3.3, we would have specified a lesser requirement.  ChimeraX requires somewhat newish hardware.  People stuck with older systems will simply have to use Chimera instead.

--Eric

[vlad_gunko@…]

Hi Eric,
There is no problem for me with OpenGL 3.3 (I could use your program with Xeon Platinum with AVX512 (+ NVIDIA, all new drivers, phys.mem. 128 Gb) with Fedora, Clear Linux or Debian), but this problem could be for other users having old PC (I tested the program on my oldest PC with maximum OpenGL 3.1) but wishing to use ChimeraX instead of Chimera. Maybe there is sense to create a version of ChimeraX which could be used with OpenGL 3.1.

Regards,
Vlad

--- Исходное сообщение ---
От кого: "Eric Pettersen" <pett@cgl.ucsf.edu>
Дата: 23 июня 2020, 03:19:35

Hi Vlad,
	I am going to break the problems you reported into separate tickets so that they can be assigned to different people and be closed individually as each problem is fixed.
	As for the OpenGL 3.3 requirement, that's what it is:  a requirement.  If we didn't need features only available in 3.3, we would have specified a lesser requirement.  ChimeraX requires somewhat newish hardware.  People stuck with older systems will simply have to use Chimera instead.

--Eric