[PyMOL] pymol autodock plugin
The autodock plugin written by Daniel Seeliger ceased to function (load) when I upgraded to Pymol 1.2r1. Although it is not compatible directly with Autodock 4, it did have the useful functionality of presenting an autodock 'box' that was readily tweakable, so that the parameters could be exported for Autodock Vina. I would LOVE to have this resurrected, but I don't know python - can anybody help with this? The specific failures I got were: File "C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py", line 16, in from Numeric import * ImportError: No module named Numeric Error: unable to initialize plugin 'autodock'. Any help would be greatly appreciated. Jed -- Jed Goldstone Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS #32 Woods Hole, MA 02543 http://www.mit.edu/people/jedgold/home.html (508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI) -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] pymol autodock plugin
Jed, With the 1.2 release of PyMOL, we have completely switched over to Numpy. So the first thing to try is to replace: from Numeric import * # with from numpy import * Cheers, Warren > -Original Message- > From: Jed Goldstone [mailto:jedg...@mit.edu] > Sent: Thursday, August 13, 2009 1:34 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] pymol autodock plugin > > The autodock plugin written by Daniel Seeliger ceased to function (load) > when I upgraded to Pymol 1.2r1. > Although it is not compatible directly with Autodock 4, it did have the > useful functionality of > presenting an autodock 'box' that was readily tweakable, so that the > parameters could be exported for > Autodock Vina. I would LOVE to have this resurrected, but I don't know > python - can anybody help with this? > > The specific failures I got were: > > File "C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py", line 16, > in > from Numeric import * > ImportError: No module named Numeric > Error: unable to initialize plugin 'autodock'. > > > Any help would be greatly appreciated. > > Jed > > -- > > Jed Goldstone > Research Specialist > Woods Hole Oceanographic Institution > Redfield 3-52 MS #32 > Woods Hole, MA 02543 > http://www.mit.edu/people/jedgold/home.html > (508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI) > > -- > > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30- > Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > ___ > 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 > > > -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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
[PyMOL] Extracting Amino Acid Sequence from PDB File
Hi All, Does anyone know of a program that can extract the amino sequence of a protein from a PDB file and output it as a FASTA file? Thanks! and all the best, --Buz -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] Extracting Amino Acid Sequence from PDB File
Buz, # Yep, PyMOL 1.2: load $TUT/1hpv.pdb save 1hpv.fasta # or by selection save 1hpv_A.fasta, chain A # etc. Cheers Warren > -Original Message- > From: Buz Barstow [mailto:b...@mac.com] > Sent: Thursday, August 13, 2009 2:39 PM > To: pymol-users@lists.sourceforge.net; ccp...@jiscmail.ac.uk > Subject: [PyMOL] Extracting Amino Acid Sequence from PDB File > > Hi All, > > Does anyone know of a program that can extract the amino sequence of a > protein from a PDB file and output it as a FASTA file? > > Thanks! and all the best, > > --Buz > > > > -- > > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30- > Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > ___ > 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 > > > -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] Extracting Amino Acid Sequence from PDB File
You can also download the sequence directly from the pdb J _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -Original Message- From: Buz Barstow [mailto:b...@mac.com] Sent: Friday, 14 August 2009 9:35 a.m. To: pymol-users@lists.sourceforge.net; ccp...@jiscmail.ac.uk Subject: [PyMOL] Extracting Amino Acid Sequence from PDB File Hi All, Does anyone know of a program that can extract the amino sequence of a protein from a PDB file and output it as a FASTA file? Thanks! and all the best, --Buz -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] PyMOL-users Digest, Vol 39, Issue 4
I was wondering if AxPyMOL could handle a .pse file that loaded two pdb structures in powerpoint. I've simply created a .pse file by fetching 2bmv and 2hhb. Then I loaded this onto my PC laptop while in powerpoint. Other slides in the same presentation with a single pdb file works fine. However, this .pse file causes AxPyMOL to crash. Any tips or suggestions would be greatly appreciated! Thanks in advance. Sean > From: pymol-users-requ...@lists.sourceforge.net > Subject: PyMOL-users Digest, Vol 39, Issue 4 > To: pymol-users@lists.sourceforge.net > Date: Tue, 11 Aug 2009 21:41:44 + > > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body 'help' to > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > >1. Re: de-speculating? (Thomas Stout) >2. figure of buried surface area (Jiamu Du) >3. Re: figure of buried surface area (Shiven Shandilya) >4. Measure surface area (Mirek Cygler) >5. Re: Measure surface area (Warren DeLano) >6. Re: Measure surface area (Robert Campbell) >7. accidently used appearance wizard, and lost my selected > sidechaine (David Shin) > > > -- > > Message: 1 > Date: Fri, 7 Aug 2009 15:54:24 -0700 > From: "Thomas Stout" > Subject: Re: [PyMOL] de-speculating? > To: "Warren DeLano" , > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > > Thanks very much, Warren. Perhaps I've dorked something in my other > settings, but I'm getting rather horrid results even with your suggestions; > I'm going to start with a fresh session and see > > -Tom > > PS - I'm "trapped" in CYMK color space since this is a job for a printing > house > > -Original Message- > From: Warren DeLano [mailto:war...@delsci.com] > Sent: Fri 8/7/2009 3:08 PM > To: Thomas Stout; pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] de-speculating? > > Hi Tom, > > > > set specular, 0 > > > > alone should be enough to do the job if all you want to do is turn off > specular lighting -- you can ignore all those other spec_* settings. > > > > However, for a more matte appearance I'd be more inclined to try: > > > > set shininess,10 > > > > set specular_intensity, 0.2 > > > > # and perhaps > > > > space pymol > > > > # in order to lessen problems with color saturation. > > > > Cheers, > > Warren > > > > > > From: Thomas Stout [mailto:tst...@exelixis.com] > Sent: Friday, August 07, 2009 2:51 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] de-speculating? > > > > > > Hi All -- > > > > Would anyone happen to have a "recipe" handy for turning down/off the > specularity (of CPK spheres especially) in PyMOL? I happen to be a fan > of more "matte" surfaces and find the highlights to be rather extreme. > I've been messing around with all of the parameters as found on > PyMOLwiki: > > > > Spec direct > > Spec direct power > > spec power > > specular > > specular intensity > > > > as well as > > reflect > > ambient > > > > et cetera > > > > but haven't really found the sweet spot. > > > > My current settings look like: > > spec_count, 1 > > spec_direct, 0.0 > > spec_direct_power, 2000 > > spec_power, 2000 > > spec_reflect, 2 > > specular, 0 > > specular_intensity, 0.5 > > ambient, 0.08 > > reflect, 0.66 > > > This is close, but loses some dimensionality in the CPK spheres (they > now look flat in the middle). Oddly, the spheres look great in the GUI > (unrendered) but the ray-traced version seems to clip the shading/color > distribution badly > > > > Any suggestions? > > > > Thanks! > > -Tom > > > > > > This email (including any attachments) may contain material > that is confidential and privileged and is for the sole use of > the intended recipient. Any review, reliance or distribution by > others or forwarding without express permission is strictly > prohibited. If you are not the intended recipient, please > contact the sender and delete all copies. > Exelixis, Inc. reserves the right, to the extent and under > circumstances permitted by applicable law, to retain, monitor > and intercept e-mail messages to and from its systems. > > > This email (including any attachments) may contain material > that is confidential and privileged and is for the sole use of > the intended recipient. Any review, reliance or distribution by > others or forwardi
