(1) Autodock Vina executable on windows (2) selection of submodels
Dear colleagues, I'd like to report a couple of issues which have cropped up. (1) On Windows, running Autodock Vina in Chimea using local executable fails due to spaces in file path (gives error something like "File "C:\Program" not found). The thing is, the university computer admins do not allow change paths or copy system files around. It should be possible to escape spaces in file names, wouldn't it? (2) The selection of submodels does not work if it is used as a part of the list. For example, "sel #1.1" selects just the submodel 1 (let's say I have a set of 20 molecules in sdf file), which is fine, while "sel #1.1,#0" selects ALL submodels in #1 in addition to #0, and that does not seem to be right. Best regards, Visvaldas
Hi Visvaldas, If you report problems, it is better to use Help… Report a Bug in the menu because it tells us what version you are using, on what platform, etc. (1) However, it looks like the same issue is already reported as a bug ticket #16322. This ticket is still open (not fixed as far as I know): <http://plato.cgl.ucsf.edu/trac/chimera/ticket/16322> (2) In this case your syntax is wrong… no # should follow the comma. So it would be: sel #1.1,0 - or - sel #0,1.1 …to get all of #0 and only submodel 1 of #1. Or if you only want 0.1 and 1.1, it would be: sel #1.1,0.1 - or - sel #0.1,1.1 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 12, 2018, at 10:05 PM, Visvaldas K. <coyote_v2002@yahoo.com> wrote:
Dear colleagues, I'd like to report a couple of issues which have cropped up.
(1) On Windows, running Autodock Vina in Chimea using local executable fails due to spaces in file path (gives error something like "File "C:\Program" not found). The thing is, the university computer admins do not allow change paths or copy system files around. It should be possible to escape spaces in file names, wouldn't it?
(2) The selection of submodels does not work if it is used as a part of the list. For example,
"sel #1.1" selects just the submodel 1 (let's say I have a set of 20 molecules in sdf file), which is fine, while "sel #1.1,#0" selects ALL submodels in #1 in addition to #0, and that does not seem to be right.
Best regards, Visvaldas
On Nov 13, 2018, at 9:41 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Visvaldas, If you report problems, it is better to use Help… Report a Bug in the menu because it tells us what version you are using, on what platform, etc.
(1) However, it looks like the same issue is already reported as a bug ticket #16322. This ticket is still open (not fixed as far as I know): <http://plato.cgl.ucsf.edu/trac/chimera/ticket/16322 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/16322>>
Hi Visvaldas, I have added you to the recipient list for that ticket. One thing you might try is to put quotes around the entire executable path in the AutoDock Vina interface. That might get it to accept a path with spaces in it. —Eric Eric Pettersen UCSF Computer Graphics Lab
Hello, On a Ubuntu 18.04.1 LTS, I get this error message when I start chimera. Is there a known fix? Am I running a too old version of chimera or should I run a version specially compiled for Ubuntu computers? Here is the full error message: --- # chimera Error while importing plipgui from /home/berenger/.local/lib/python2.7/site-packages: Traceback (most recent call last): File "/home/berenger/usr/chimera-1.12/share/chimera/extension/base.py", line 349, in _importExtension __import__(module) File "/home/berenger/.local/lib/python2.7/site-packages/plipgui/ChimeraExtension.py", line 8, in <module> from plipgui.core import cmd_plip, cmd_unplip File "/home/berenger/.local/lib/python2.7/site-packages/plipgui/core.py", line 50, in <module> from plip.modules.preparation import PDBComplex File "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/preparation.py", line 13, in <module> from .detection import * File "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/detection.py", line 12, in <module> from .supplemental import * File "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/supplemental.py", line 26, in <module> import pybel File "/home/berenger/.local/lib/python2.7/site-packages/pybel.py", line 53, in <module> import openbabel as ob File "/home/berenger/.local/lib/python2.7/site-packages/openbabel.py", line 21, in <module> _openbabel = swig_import_helper() File "/home/berenger/.local/lib/python2.7/site-packages/openbabel.py", line 20, in swig_import_helper return importlib.import_module('_openbabel') File "/home/berenger/usr/chimera-1.12/lib/python2.7/importlib/__init__.py", line 37, in import_module __import__(name) ImportError: /home/berenger/usr/chimera-1.12/lib/libgomp.so.1: version `GOMP_4.0' not found (required by /usr/lib/libopenbabel.so.4) --- Thanks a lot, F.
That looks like a problem between libopenbabel and Chimera. The bug is that libopenbabel.so was compiled with a newer compiler than what Chimera was compiled with. You can try renaming chimera-1.12/lib/libgomp.so.1 (eg., to libgomp.so.1.save) to see if it fixes the problem. While I consider this a bug with the Python openbabel package, it should be bundling and using a libopenbabel.so that is compatible with the Python "manylinux1" ABI (based on CentOS 5), we will investigate incorporating a workaround. -- Greg On 11/13/2018 5:53 PM, Francois Berenger wrote:
Hello,
On a Ubuntu 18.04.1 LTS, I get this error message when I start chimera.
Is there a known fix?
Am I running a too old version of chimera or should I run a version specially compiled for Ubuntu computers?
Here is the full error message: --- # chimera Error while importing plipgui from /home/berenger/.local/lib/python2.7/site-packages: Traceback (most recent call last): File "/home/berenger/usr/chimera-1.12/share/chimera/extension/base.py", line 349, in _importExtension __import__(module) File "/home/berenger/.local/lib/python2.7/site-packages/plipgui/ChimeraExtension.py", line 8, in <module> from plipgui.core import cmd_plip, cmd_unplip File "/home/berenger/.local/lib/python2.7/site-packages/plipgui/core.py", line 50, in <module> from plip.modules.preparation import PDBComplex File "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/preparation.py", line 13, in <module> from .detection import * File "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/detection.py", line 12, in <module> from .supplemental import * File "/home/berenger/.local/lib/python2.7/site-packages/plip/modules/supplemental.py", line 26, in <module> import pybel File "/home/berenger/.local/lib/python2.7/site-packages/pybel.py", line 53, in <module> import openbabel as ob File "/home/berenger/.local/lib/python2.7/site-packages/openbabel.py", line 21, in <module> _openbabel = swig_import_helper() File "/home/berenger/.local/lib/python2.7/site-packages/openbabel.py", line 20, in swig_import_helper return importlib.import_module('_openbabel') File "/home/berenger/usr/chimera-1.12/lib/python2.7/importlib/__init__.py", line 37, in import_module __import__(name) ImportError: /home/berenger/usr/chimera-1.12/lib/libgomp.so.1: version `GOMP_4.0' not found (required by /usr/lib/libopenbabel.so.4) ---
Thanks a lot, F.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (5)
-
Elaine Meng -
Eric Pettersen -
Francois Berenger -
Greg Couch -
Visvaldas K.