Re: [PyMOL] Logging the sculpt wizard
Hi Martin, I have a script that does almost exactly what you want (I guess). See attachment. Cheers, Thomas On Wed, Mar 23, 2011 at 11:19 PM, Martin Hediger ma@bluewin.ch wrote: Dear List I'm trying to automate the following sequence of steps in a PyMOL python script: 1. Start the mutagenesis wizard 2. Mutate a reside according to an input from the script (some integer to specify the id) 3. Apply and close the mutagenesis wizard 4. Start the Sculpt Wizard 5. Fix all coordinates but the residue just mutated 6. Start the sculpt algorithm to get a rough optimization of the side chain 7. End the sculpt algorithm and close the sculpt wizard. 8. Save the structure to a new file. I have the steps up to 3. ready in a script for generation of variants. However, when running a log file while performing steps 4. onwards, there are no commands written into the log file for the sculpting functions. Pressing the Sculpt button in the PyMOLX11Hybrid does not lead to a command I can see in the log file. What would be the Python code to start the sculpt process? Any hints are welcome. Thanks a lot. -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen mutate.py Description: Binary data -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to get pymol 1.4
Hi Jason, many thanks for your reply and efforts. I hope you have a good time at the meetings. Keep up the good work !! cheers, Abhi On Wed, Mar 23, 2011 at 8:06 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Stephen, I would like to know if, and when, 1.4 will be available for downloading. Yes, PyMOL v1.4 will be released to the open-source. I will prepare the v1.4 release file soon (hopefully less than two weeks' time). As Michael noted, it's nothing insidious: within hours of releasing the v1.4 to the incentive users, I had to get in a plane and fly to the west coast to present and support PyMOL. I'm at the crystallographic WCPCW meeting this week, and ACS next week. When I return home, I'll merge the volumes code and make the release file. I'll announce it when I finish and it's posted. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Logging the sculpt wizard
there was a bug in the script, sorry. Corrected script attached. Cheers, Thomas On Thu, Mar 24, 2011 at 8:40 AM, Thomas Holder spel...@users.sourceforge.net wrote: Hi Martin, I have a script that does almost exactly what you want (I guess). See attachment. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen mutate.py Description: Binary data -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PovRay
Hi Ian,
As this may be of broader interest, I forward it to the pymol user list too.
You can clip the scene using an intersection. Let's say that you have
the object you want to clip stored as a povray include file
object.inc. Then you can get the clipped object as:
//###
pymol_object = union { #include object.inc }
clip = ...; // Here you need to fill in the 16th number from
get_view(), giving the distance of the front clipping plane
intersection { object { pymol_object } plane { z, -clip } }
//###
The plane could also be defined as plane{z,0 translate -clip} or,
along the same lines, as plane{z,0 rotate 30*y translate-clip}. Like
that you can have the clipping plane rotated.
Do note that such intersections are often very slow. Especially with
meshes (like surfaces) it is likely to be a pain (but potentially
yielding great imagery :)). With many separate objects, spheres in
particular, you can clip each of them separately, which is much
faster, especially if you use the directives 'bounded_by' and
'clipped_by'. For a sphere defined as
sphere{0,0,0, 1 pigment{color rgb 1}}
this means that you convert it to
intersection{
sphere{0,0,0, 1}
object{IntersectionObject}
pigment{color rgb 1}
bounded_by { sphere{0,0,0, 1} }
}
I would suggest scripting this... :)
Hope it helps, and good luck!
Cheers,
Tsjerk
On Thu, Mar 24, 2011 at 8:31 PM, Ian Slaymaker iamslayma...@gmail.com wrote:
Dear Tsjerk,
I apologize for the elementary nature of my question, but I have spent quite
some time wrestling with my rendering issues, and after solving most of
them, a very small issue is blocking my progress. How do you get PovRay to
read in the clipping plan of a pymol scene? I have tried a number of things,
and nothing seems to work. Any help would be greatly appreciated. Thank you.
Best,
Ian
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[PyMOL] MacPyMOL 1.4 on OS X 10.5.8 load command error
Hi Jason et al, We just added PyMOL 1.4 to our software environment, and it looks like Numpy doesn't want to run on 10.5.8 machines: PyMOLimport numpy Traceback (most recent call last): File /programs/m/pymol/1.4/MacPyMOL.app/pymol/modules/pymol/parser.py, line 260, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1, in module File /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/__init__.py, line 136, in module import add_newdocs File /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/add_newdocs.py, line 9, in module from numpy.lib import add_newdoc File /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/lib/__init__.py, line 4, in module from type_check import * File /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/lib/type_check.py, line 8, in module import numpy.core.numeric as _nx File /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/core/__init__.py, line 5, in module import multiarray ImportError: dlopen(/programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/core/multiarray.so, 2): no suitable image found. Did find: /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/core/multiarray.so: unknown required load command 0x8022 There's some info about this error in this thread on Xcode-users: http://lists.apple.com/archives/Xcode-users/2009/Oct/msg00514.html And a page about the compressed linkedit loader commands which are the root cause here: http://networkpx.blogspot.com/2009/09/about-lcdyldinfoonly-command.html The fix is not entirely clear to me by looking at those sources. It looks like you'll have to experiment a bit if you want to continue to support 10.5 users. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Reminder: Fourth annual CCP4 summer school in USA, at APS, June 7-15
Dear Colleagues, This is a reminder that the deadline for applications for the 4th annual CCP4 summer school From data collection to structure refinement and beyond is April 8. The school will take place June 7-15, 2011 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (the program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2011/ The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] MacPyMOL 1.4 on OS X 10.5.8 load command error
Hi Ben, Thanks for finding this. A colleague looked into this and says it's fixable. So, we'll have a fix out soon. This is a 10.5-specific numpy issue. Our update release is planned to follow soon to clear up a few small issues. Cheers, -- Jason On Thu, Mar 24, 2011 at 3:42 PM, Ben Eisenbraun b...@hkl.hms.harvard.edu wrote: Hi Jason et al, We just added PyMOL 1.4 to our software environment, and it looks like Numpy doesn't want to run on 10.5.8 machines: PyMOLimport numpy Traceback (most recent call last): File /programs/m/pymol/1.4/MacPyMOL.app/pymol/modules/pymol/parser.py, line 260, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1, in module File /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/__init__.py, line 136, in module import add_newdocs File /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/add_newdocs.py, line 9, in module from numpy.lib import add_newdoc File /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/lib/__init__.py, line 4, in module from type_check import * File /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/lib/type_check.py, line 8, in module import numpy.core.numeric as _nx File /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/core/__init__.py, line 5, in module import multiarray ImportError: dlopen(/programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/core/multiarray.so, 2): no suitable image found. Did find: /programs/m/pymol/1.4/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/numpy/core/multiarray.so: unknown required load command 0x8022 There's some info about this error in this thread on Xcode-users: http://lists.apple.com/archives/Xcode-users/2009/Oct/msg00514.html And a page about the compressed linkedit loader commands which are the root cause here: http://networkpx.blogspot.com/2009/09/about-lcdyldinfoonly-command.html The fix is not entirely clear to me by looking at those sources. It looks like you'll have to experiment a bit if you want to continue to support 10.5 users. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
