Re: [PyMOL] Secondary structure for C-alpha only and coarse-grained models
Thanks a lot Tsjerk,
It iw really going to be helpful. I will update you when I play with it.
best,
Abhi
On Sat, Nov 9, 2013 at 12:46 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hey :)
I thought there was a post recently about showing secondary structure in
C-alpha only models. I can't find it anymore, but in any case it's
something popping up now and again. For reconstruction of high-resolution
models out of coarse-grained ones, I came up with a very simple algorithm
for rebuilding the backbone based on C-alpha atoms only. I realized that
that could work for determining secondary structure, and made a function
out of it. It's not perfect, as sometimes a residue gets a flipped
backbone, but overall it seems to work pretty nicely. The following can be
put in a script (bbpredict.py):
from pymol import cmd
import math
def oprod(a,b): return
a[1]*b[2]-a[2]*b[1],a[2]*b[0]-a[0]*b[2],a[0]*b[1]-a[1]*b[0]
def vsub(a,b): return [i-j for i,j in zip(a,b)]
def cest(u,v,w): return [i+0.37*j+0.45*k for i,j,k in zip(u,v,w)]
def oest(u,v,w): return [i+0.37*j+1.75*k for i,j,k in zip(u,v,w)]
def hest(u,v,w): return [i-0.37*j-1.45*k for i,j,k in zip(u,v,w)]
def nest(u,v,w): return [i-0.37*j-0.45*k for i,j,k in zip(u,v,w)]
def norm(a): return math.sqrt(sum([i**2 for i in a]))
def vdiv(a,b): return [i/b for i in a]
def bbpredict(selection,name=bbpred):
m=cmd.get_model(selection+' and n. ca')
x=m.get_coord_list()
d=[(vsub(j,i),vsub(k,i)) for i,j,k in zip(x,x[1:],x[2:])]
o=[oprod(*i) for i in d]
no=[vdiv(i,norm(i)) for i in o]
CA = [(ATOM %5d CA %3s %1s%4d+(%8.3f%8.3f%8.3f%tuple(i)))
for i in x]
N = [(ATOM %5d N %3s %1s%4d
+(%8.3f%8.3f%8.3f%tuple(nest(i,j[0],k for i,j,k in zip(x[1:],d,no)]
H = [(ATOM %5d H %3s %1s%4d
+(%8.3f%8.3f%8.3f%tuple(hest(i,j[0],k for i,j,k in zip(x[1:],d,no)]
C = [(ATOM %5d C %3s %1s%4d
+(%8.3f%8.3f%8.3f%tuple(cest(i,j[0],k for i,j,k in zip(x,d,no)]
O = [(ATOM %5d O %3s %1s%4d
+(%8.3f%8.3f%8.3f%tuple(oest(i,j[0],k for i,j,k in zip(x,d,no)]
j = m.atom[0]
bb= [CA[0]%(3,j.resn,j.chain,int(j.resi))]
bb.append(C[0]%(4,j.resn,j.chain,int(j.resi)))
bb.append(O[0]%(5,j.resn,j.chain,int(j.resi)))
stuff = zip(m.atom[1:],zip(N,H,CA[1:],C[1:],O[1:]))
bb.extend([ i%(num,j.resn,j.chain,int(j.resi)) for j,k in stuff for
i,num in zip(k,range(5)) ])
cmd.read_pdbstr(\n.join(bb),name)
END
Then it can be used e.g. as follows (yes, a full atomistic structure for
demonstration):
run bbpredict.py
fetch 6lzm
bbpredict('6lzm','pred')
dss pred
I'll see if I can get the flips out and tidy the code up a bit. Then I'll
add this to the wiki. I hope it'll be of some use to anyone. The routine is
explained in a manuscript we just submitted.
Cheers,
Tsjerk
--
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Re: [PyMOL] problems with mutagenesis wizard
can you give us the exact pdb/code so that we can reproduce the problem ? On Fri, Jun 1, 2012 at 11:16 AM, James Starlight jmsstarli...@gmail.comwrote: Dear PyMol users! I've tried to make 1 point mutation by means of pymol's mutagenesis wizard and obtain partially broken pdb. In my caseI've changed 276 residue from Leu to Tyr. As the consequence the resulted pdb consist of wrong atom order ( you can see it inthe below where new mutaded tyr is mixed with the atoms of the firstr residue and partly with the atoms of second residue of that protein ( met-2 and gly-3 in that pdb). ATOM 1 N MET 2 30.865 33.218 71.898 1.00 0.00 N ATOM 0 N TYR 276 36.846 30.673 29.037 1.00 0.00 N ATOM 2 H MET 2 30.860 32.973 70.919 1.00 0.00 H ATOM 1 CA TYR 276 38.223 31.049 28.728 1.00 0.00 C ATOM 3 CA MET 2 30.563 32.110 72.824 1.00 0.00 C ATOM 2 CB TYR 276 38.572 32.435 29.346 1.00 0.00 C ATOM 4 CB MET 2 29.075 32.007 73.159 1.00 0.00 C ATOM 3 CG TYR 276 38.566 32.527 30.876 1.00 0.00 C ATOM 5 CG MET 2 28.699 32.785 74.409 1.00 0.00 C ATOM 4 CD1 TYR 276 39.655 32.065 31.622 1.00 0.00 C ATOM 6 SD MET 2 27.037 32.348 75.030 1.00 0.00 S ATOM 5 CD2 TYR 276 37.467 33.087 31.534 1.00 0.00 C ATOM 7 CE MET 2 27.384 30.784 75.811 1.00 0.00 C ATOM 6 CE1 TYR 276 39.644 32.168 33.011 1.00 0.00 C ATOM 8 C MET 2 31.021 30.724 72.375 1.00 0.00 C ATOM 7 CE2 TYR 276 37.458 33.188 32.922 1.00 0.00 C ATOM 9 O MET 2 31.124 30.414 71.189 1.00 0.00 O ATOM 8 CZ TYR 276 38.547 32.729 33.660 1.00 0.00 C ATOM 10 N GLY 3 31.434 29.985 73.384 1.00 0.00 N ATOM 9 OH TYR 276 38.542 32.830 35.022 1.00 0.00 O ATOM 11 H GLY 3 31.957 30.390 74.138 1.00 0.00 H ATOM 10 C TYR 276 39.196 30.036 29.278 1.00 0.00 C ATOM 12 CA GLY 3 31.510 28.518 73.329 1.00 0.00 C ATOM 11 O TYR 276 40.317 29.796 28.774 1.00 0.00 O As the result when I've tried to process this pdb via Gromacs I've obtained incorrect atom numbering etc. How this error could be fixed ? Thanks, James -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ 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] list of polar contacts
Great!! Thanks to all !!.. and specially Takanori!! Cheers, Abhi On Wed, Feb 1, 2012 at 6:09 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Thomas, alternate locations and multi-state objects should not be an issue, the script on the PyMOLWiki can handle both! The only issue would be altering coordinates after distance objects have been created (and having dynamic_measures = off). I just read over your change to Takanori's original script. Nice work -- you did indeed take care of those issues. Cheers, -- Jason On Wed, Feb 1, 2012 at 12:00 PM, Thomas Holder spel...@users.sourceforge.net wrote: Jason, Nevertheless, I'm glad you plan to provide a real C-object solution, looking forward to this! Cheers, Thomas On 02/01/2012 05:46 PM, Jason Vertrees wrote: Thomas, When you hash by coordinates you could get odd results from alternate locations and multi-state objects. I like how Takanori solved the problem, but it's not a strictly perfect solution. What I need to do is provide access to the C-object for real. We plan to provide something for this soon. Cheers, -- Jason -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ 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 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ 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] list of polar contacts
Hi thanks, still it is not the same.. But thanks.. I wish Jason can reply if there is any way to get the list from the apply command. thanks, Abhi On Mon, Jan 30, 2012 at 5:53 PM, Thomas Evangelidis teva...@gmail.comwrote: I think you can reproduce the results from apply-find-polar contacts option with the PyMOL built-in distance command. E.g. distance hbonds, all, all, 3.2, mode=2 The problem is that you cannot set the A-H-D angle which is important for the definition of the H-bond. On 30 January 2012 18:45, Abhinav Verma abhinav1...@gmail.com wrote: Thanks Thomas, I have been here and my problem is that I could not reproduce the results of default pymol behaviour. I just need to either reproduce 100% the pymol default behaviour or to just get a list of what is painted in the window. It should be possible I guess. Do you have more ideas? On Mon, Jan 30, 2012 at 5:38 PM, Thomas Evangelidis teva...@gmail.comwrote: Probably because they set diffently the acceptor-donor cutoff and the acceptor-hydrogen-donor angle. Use list_hbonds.py from: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ and set the cutoff and angle to the values you wish. Thomas On 30 January 2012 16:34, Abhinav Verma abhinav1...@gmail.com wrote: Hi, I am trying to get the list of hbonds formed using Apply-find-polarcontacts. I searched and found some scripts, but they never give me the same result as the one by default pymol. Any ideas how I can get the hbonds as a list. Thanks, Abhinav -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ 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 -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ 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 -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d___ 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] list of polar contacts
Hi, I am trying to get the list of hbonds formed using Apply-find-polarcontacts. I searched and found some scripts, but they never give me the same result as the one by default pymol. Any ideas how I can get the hbonds as a list. Thanks, Abhinav -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ 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] distance bug
Hi, My pymol 1.4.1 works fine. can you try to ray trace and see if your objects are available but just not displayed on the standard screen? cheers, 2011/9/29 Andreas Förster docandr...@gmail.com Hi all, Has anyone noticed that the distance command behaves oddly. Has this been recently introduced? fetch 1ubq zoom 1ubq dist 9/cg2, 73/cd2 # output: object dist01 is created # distance of 10.2 is shown, but no dashed line # now check this out: # several repetitions of the next two lines disable dist01 enable dist01 # eventually lead to the appearance of the dashed line # but it gets better disable dist01 enable dist01 # The distance is enabled but neither number nor dashed line are visible disable dist01 enable dist01 # Now the number and the dashed line are back When dist01 is enabled but invisible, disabling 1ubq brings it back, but it disappears again when 1ubq is re-enabled. With other pdb files, the distance command doesn't work at all. It returns a distance of 0.0A to the screen that is only visible when the associated pdb object is disabled. I've observed this with pymol-py26 1.4-7 installed with fink on a MacBook running 10.6 and with pymol 1.4.1 revision 3968 installed through svn on RHEL 6.1 Notably, earlier revisions (e.g. 3958 and 3945) on RHEL 6.1 work just fine. Recently introduced bug? Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1___ 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] format problem
As Tsjerk pointed out!!.. it is exactly 8.3 ATOM604 OG SER A 77 37.493 60.526-103.507 1.00 26.47 O 123456781234567812345678 cheers, Abhi On Mon, Apr 25, 2011 at 12:59 PM, kanika sharma ksharma...@gmail.comwrote: in the y-z coordinate the 8.3% format is not there.. On Mon, Apr 25, 2011 at 4:09 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Kanika, No, the spacing, or in this case the lack of it, is correct. The coordinate section of the pdb file is %8.3f%8.3f%8.3f, i.e. each coordinate eight characters wide with three decimal precision. Cheers, Tsjerk On Mon, Apr 25, 2011 at 12:28 PM, kanika sharma ksharma...@gmail.com wrote: i have attached a small section of the file after applying the matrix.. the spacing between x,y and z axis is abnormal -- 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 -- Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails ___ 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 -- Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails___ 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] segmentation fault pymol 1.4 rev 3938
Hi Jason Tsjerk ... Just for the info that I just downloaded, compiled and tried it on OpenSuse 11.4 and it ran without any problems: PyMOLload ../../3lzt.pdb HEADERHYDROLASE 23-MAR-97 3LZT TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION COMPNDMOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. Symmetry: Found 1 symmetry operators. ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom, unsuccessful in guessing valences. CmdLoad: ../../3lzt.pdb loaded as 3lzt. hth, abhi On Mon, Apr 11, 2011 at 9:43 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jason, I run into a segfault with Pymol 1.4 rev 3938 on my EEE PC, running Ubuntu 9.04. The segfault occurs when loading the PDB file. It happens regardless of the contents of the PDB file, but loading something with hetatms gives some insight in how far it goes: PyMOLload ../../../3lzt.pdb HEADERHYDROLASE 23-MAR-97 3LZT TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION COMPNDMOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.17; COMPND 5 OTHER_DETAILS: NITRATE AND ACETATE IONS PRESENT ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. Symmetry: Found 1 symmetry operators. ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom, unsuccessful in guessing valences. Segmentation fault If you need any information on libraries or such, let me know. Best, Tsjerk -- 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 -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ 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 -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev___ 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 Project Updates Open Source PyMOL v1.4b1
Thanks a lot Jason!! Will try it out today!! On Fri, Apr 1, 2011 at 11:34 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Greetings PyMOLers, I got back from my trip last night and immediately started putting the new features into the open source branch as promised. I've finished the merge, pushed the changes to SourceForge (revision 3938), and uploaded a tar file (https://sourceforge.net/projects/pymol/files/pymol/1.4/). I'm calling this v1.4b1 (beta one) on the SourceForge site. We will collect bug reports from you, the community, and then release the stable v1.4 official code once the serious bugs are fixed. Additionally, in order to improve communication and openness, I've re-enabled the SourceForge bug tracker (https://sourceforge.net/tracker/?group_id=4546atid=104546). If someone would like to act as a good steward and help manage the tracker, please let me know. This will help us stay on top of the open-source bugs. For those adventurous enough to try the new code please give it a shot. If you're not familiar with building PyMOL, please wait for the stable v1.4 release. For those wishing to try the new beta release these following notes might help: (1) If you're building from source, please install * glew * glew-devel as they're new dependencies. I'm using glew 1.5.8 on OpenSuSE 11.3. (2) This update requires your hardware to support OpenGL 2.0+. There are known problems running this from within a VM. I think Parallels does handle openGL 2.0+, but VMWare does not yet support it. (3) Please update your video card drivers. My build just failed to compile shaders (at run time) because I had the wrong drivers installed! (4) Volumes don't yet ray trace, but they will soon. For a nice image, set use_shaders and also try, Display Quality Maximum Quality before using the png command to save the image. (5) cealign is properly integrated and memory leaks and crashing should be fixed. (6) I only made changes to the Linux portion of the setup.sh file. If you're daring enough on Mac/Fink feel free to try get the build working there, too. (7) The 'svn diff' from the last revision is 12000+ lines long, so there's quite a few changes. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ 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 -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ 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
[PyMOL] How to get pymol 1.4
How do I download pymol 1.4 from the svn. I used svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol but i still got the 1.3 version. Is the 1.4 version restricted to incentive downloads only?? Thanks, -- 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
And why would that be? I thought that pymol is open source and till Warren was there all updates were available in the open source domain and incentive builds were limited to windows executable and involving support!! On Wed, Mar 23, 2011 at 11:15 AM, Mark J van Raaij mjvanra...@cnb.csic.eswrote: Is the 1.4 version restricted to incentive downloads only?? Yes Thanks, -- 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] How to get pymol 1.4
Thanks for pointing out Jason's email. I missed that. And at the same time I shall learn to read and understand the fine-print under open source. On Wed, Mar 23, 2011 at 12:12 PM, li...@cowsandmilk.net wrote: a) you're mistaken, Warren's incentive builds had extra features. Also, Warren had announced pretty clear plans of adding more features to the incentive builds and not releasing them open source for several years b) if you've been following the list, Jason has stated that many of the 1.4 features are on their way to the open source repository. Sure, I am of the type that wishes all features were open source and that Jason did all development directly against a repository we could all see, but I think he's done a good job communicating the way development is happening to the list and schrodinger's model for the incentive builds seems to be hardly different from what Warren had started doing. -David On Mar 23, 2011, at 6:33 AM, Abhinav Verma abhinav1...@gmail.com wrote: And why would that be? I thought that pymol is open source and till Warren was there all updates were available in the open source domain and incentive builds were limited to windows executable and involving support!! On Wed, Mar 23, 2011 at 11:15 AM, Mark J van Raaij mjvanra...@cnb.csic.es mjvanra...@cnb.csic.es wrote: Is the 1.4 version restricted to incentive downloads only?? Yes Thanks, -- 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___ http://p.sf.net/sfu/intel-dev2devmar___ PyMOL-users mailing list ( PyMOL-users@lists.sourceforge.net PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net 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 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 https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net 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
[PyMOL] Fwd: coloring labels
set label_color, black can help you. Abhi On Tue, Aug 31, 2010 at 6:31 AM, Craig Smith boiler...@mac.com wrote: Hello, I'm to make the color of my label different from the color of the residue. For example, I have my carbons colored yellow but its label is hard to see and I want to change the color to black. How do I do this? Craig -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ 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 -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd___ 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] Using povray with pymol
Hi Tsjerk, Thanks a lot for reply.. All I wanted to try was to use povray instead of pymol's internal ray tracer. Now if you type help povray, it will come with a suggestion to use an age old patch and use smooth_color. PyMOLhelp povray DESCRIPTION PovRay: Persistance of Vision Support Information (EXPERIMENTAL) The built-in ray-tracer (technically a ray-caster) is as fast or faster than PovRay for most figures (provided that hash_max is tuned for your system). However, PovRay blows PyMOL away when it comes to rendering images without using lots of RAM, and with PovRay you get the ability use perspective, textures, reflections, infinite objects, and a superior lighting model. PovRay does not include interpolated colors within triangles (!!), so you must patch the source code in order to obtain this basic functionality required for rendering molecular surfaces. Details can be found on the DINO website. http://www.biozentrum.unibas.ch/~xray/dino To use PovRay, you must be running under Unix and have x-povray in your path. Unfortunately, the developers of PovRay do not share PyMOL's open-source philosophy, so you will need to download, configure, patch (for smooth_color_triangles), and install it yourself. Despite being free and open-source, PovRay's license prevents it from being modified or conveniently combined with PyMOL, and thus it serves as a textbook example for why open-source licenses should be wholly non-restrictive. Assuming that PovRay is built and in your path... ray renderer=1 # will use PovRay instead of the built-in engine set ray_default_renderer=1 # changes the default renderer to PovRay ray # will now use PovRay by default cmd.get_povray() # will give you a tuple of PovRay input strings # which you can manipulate from Python set smooth_color_triangles = 1 # is required in order to get decent surfaces in PovRay. You must patch PovRay first. so I tired that link (the patch was moved since then to another address) http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00868.html but all that is useless since smooth_color_triangle itself doesnt exist. I tried to change it to smooth_triangle and still povray didnt do anything. So Now I tried your suggestions of manually editing the file and changing some settings .. but I am not getting the result yet.. I am linking 3 pictures. 1. internal ray tracer ( http://picasaweb.google.com/lh/photo/c9LUJwzPEYjpVVC0ThkQhQ?feat=directlink) 2. using ray renderer=1 for povray ( http://picasaweb.google.com/lh/photo/0736f1oK9dRaB8fV7Zmm6g?feat=directlink) 3. applying ur settings ( http://picasaweb.google.com/lh/photo/udk9a4AzhpdI2RfQvclciw?feat=directlink) Pymol should probably update the help povray description so that it does not mislead anymore. Thanks !! Abhi On Mon, May 18, 2009 at 11:55 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Abhi, I had a look and found that POV-Ray does not have a keyword 'smooth_color_triangle' (anymore), but this should be changed to 'smooth_triangle'. Also, the mesh2 object Pymol writes already for ages is far superior to a set of smooth_triangles. This leaves me a bit puzzled as what it is you mean. Could you link/post an example of the image as you get now and indicate what you want to have different? Maybe also try the change in lighting and finish I posted a few days ago on the list. It may well be that the default POV-Ray settings pymol uses for light and appearance are causing the problem. Cheers, Tsjerk On Mon, May 11, 2009 at 5:41 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Abhi, I got and read the e-mail through the list, but would have to test with pymol 1.0 before being able to give a sensible reply. As I'm now underway that's a bit too much for me :) I'll come back on this one later. By the way, you only sent this mail this afternoon. Don't expect instant replies or assume something didn't come through just because you didn't get an answer within a few hours :) Cheers, Tsjerk On Mon, May 11, 2009 at 5:05 PM, Abhinav Verma abhinav1...@gmail.com wrote: Hi Tsjerk, I am sending this email personally to you (sorry for that). I am sorry, but I posted it to pymol mailing list but it seems to have been stuck somewhere. Any idea would be helpful, thanks, Abhi -- Forwarded message -- From: Abhinav Verma abhinav1...@gmail.com Date: Mon, May 11, 2009 at 3:06 PM Subject: Using povray with pymol To: pymol-users pymol-users@lists.sourceforge.net I am trying to use povray tracer with pymol. I got povray and installed it and tried to follow the instructions for the patch.. The patch seems too old written in 1999 and the current povray code is cpp and not c. so I skipped that part
Re: [PyMOL] Using povray with pymol
Hi Tsjerk!!, Yes,, it is really an oldie.. ( I tried to patch, but the new code is cpp and not c anymore for povray, so I left the oldie goldie ). All I need is to get close to pymol trace.. i.e. the shine which is missing in my links to the pictures in my previous mail (this is just a very simple example i just created to illustrate. But as the detail in a picture increases the effect of ligting and shine also will change. Pymol's internal ray tracer nearly always justice to these details, but as mentioned can have memory issues for large pictures. So I need to go to povray to get my job done. The settings you suggested, I just used those blindly at the moment ( I will play with those in the coming days). I wish I could write a povray file which by default does justice to the picture generated. by povray when compared to internal ray tracer. thanks again for your help. Abhi. On Mon, May 18, 2009 at 4:58 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Abhi, Oooh, that's an oldie alright. I only vaguely recollect that coming in :) But you need to patch POV-Ray for it... Anyway, the mesh2 object also allows for smoothly colored triangles, so in that sense there's no need to really do it. The big question is really what do you want to see and what do get instead? Cheers, Tsjerk On Mon, May 18, 2009 at 4:53 PM, Abhinav Verma abhinav1...@gmail.com wrote: Hi Tsjerk, Thanks a lot for reply.. All I wanted to try was to use povray instead of pymol's internal ray tracer. Now if you type help povray, it will come with a suggestion to use an age old patch and use smooth_color. PyMOLhelp povray DESCRIPTION PovRay: Persistance of Vision Support Information (EXPERIMENTAL) The built-in ray-tracer (technically a ray-caster) is as fast or faster than PovRay for most figures (provided that hash_max is tuned for your system). However, PovRay blows PyMOL away when it comes to rendering images without using lots of RAM, and with PovRay you get the ability use perspective, textures, reflections, infinite objects, and a superior lighting model. PovRay does not include interpolated colors within triangles (!!), so you must patch the source code in order to obtain this basic functionality required for rendering molecular surfaces. Details can be found on the DINO website. http://www.biozentrum.unibas.ch/~xray/dinohttp://www.biozentrum.unibas.ch/%7Exray/dino To use PovRay, you must be running under Unix and have x-povray in your path. Unfortunately, the developers of PovRay do not share PyMOL's open-source philosophy, so you will need to download, configure, patch (for smooth_color_triangles), and install it yourself. Despite being free and open-source, PovRay's license prevents it from being modified or conveniently combined with PyMOL, and thus it serves as a textbook example for why open-source licenses should be wholly non-restrictive. Assuming that PovRay is built and in your path... ray renderer=1 # will use PovRay instead of the built-in engine set ray_default_renderer=1 # changes the default renderer to PovRay ray # will now use PovRay by default cmd.get_povray() # will give you a tuple of PovRay input strings # which you can manipulate from Python set smooth_color_triangles = 1 # is required in order to get decent surfaces in PovRay. You must patch PovRay first. so I tired that link (the patch was moved since then to another address) http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00868.html but all that is useless since smooth_color_triangle itself doesnt exist. I tried to change it to smooth_triangle and still povray didnt do anything. So Now I tried your suggestions of manually editing the file and changing some settings .. but I am not getting the result yet.. I am linking 3 pictures. 1. internal ray tracer ( http://picasaweb.google.com/lh/photo/c9LUJwzPEYjpVVC0ThkQhQ?feat=directlink ) 2. using ray renderer=1 for povray ( http://picasaweb.google.com/lh/photo/0736f1oK9dRaB8fV7Zmm6g?feat=directlink ) 3. applying ur settings ( http://picasaweb.google.com/lh/photo/udk9a4AzhpdI2RfQvclciw?feat=directlink ) Pymol should probably update the help povray description so that it does not mislead anymore. Thanks !! Abhi On Mon, May 18, 2009 at 11:55 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Abhi, I had a look and found that POV-Ray does not have a keyword 'smooth_color_triangle' (anymore), but this should be changed to 'smooth_triangle'. Also, the mesh2 object Pymol writes already for ages is far superior to a set of smooth_triangles. This leaves me a bit puzzled as what it is you mean. Could you link/post
[PyMOL] Using povray with pymol
I am trying to use povray tracer with pymol. I got povray and installed it
and tried to follow the instructions for the patch.. The patch seems too old
written in 1999 and the current povray code is cpp and not c. so I skipped
that part.. and now when I set smooth_color_triangle = 1, I get the
following parse error..
pigment{color rgb1.1,0.0904,0.}}
mesh {
smooth_color_triangle
Parse Error: No triangles in triangle mesh.
If I donot swich it on, I get really ugly colored picture from the
tmp_povray.pov file generated by pymol.
Any Ideas to get similars colors that comes with pymol inbuild ray tracer
and use povray ( I want to use povray as pymol is crashing because of size )
Thanks in advance,
Abhi
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Re: [PyMOL] partial alignment (super?)
or if B' is residues M to N in prot1 and B'' is residues L to K in prot2, its as simple as load prot1.pdb load prot2.pdb align prot1 and i. M-N, prot2 and i. L-K look at help selections and you can try to align any two selections.. cheers, Abhi. On Thu, Mar 20, 2008 at 12:34 PM, DeLano Scientific del...@delsci.info wrote: Carlo, If B is the chain ID for the matched seguments, then it should be as simple as: load file1.pdb load file2.pdb align file1//B//CA, file2//B//CA Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Carlo Zambonelli Sent: Thursday, March 20, 2008 11:37 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] partial alignment (super?) Hi, I have 2 pdb files corresponding to 2 partially overlapping proteins: AB' and BC. B' and B have similar but not identical structures. I want to align B' and B so to obtain ABC. Can I select to align only portions of molecules? Another possibility is to create 2 new pdb files corresponding to B' and B, do the alignment and then attach back A and C, even though I'm not completely sure after importing A and C in the B'-B alignment session, how I would correctly position A and C with their original orientations relative to B' and B. Thank you for your help! Carlo -- --- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Abhianv Verma Research Associate, Daggett Lab, Benjamin Hall Interdisciplinary Research Building University of Washington Box 355013 Seattle, WA 98195-5013
Re: [PyMOL] matching colors
you can try to use a pick-color tool of corel draw.. I am not sure what it is actually called in corel, but you might be able to pick the exact colors with that tool... hth, Abhi. On Wed, Mar 5, 2008 at 2:17 PM, Patrick Loll pat.l...@drexel.edu wrote: I'm making a figure that contains both an actual molecular representation (from PyMOL) and a simplified cartoon representation of the same complex (made in a graphics program, in this case CorelDraw). I want to match the colors between the two parts of the figure (or at least get close). However, while I can get a decent match for primary colors (red, yellow), for colors like magenta, cyan, light green, and purple, I can't get anywhere close--the colors in the PyMOL picture are rich and vibrant, while my best attempts to match them in CorelDraw are VERY far off and dull and nasty. Any ideas? E.g., can someone point me to the RGB or CMYK mappings for the different colors used in PyMOL? I can choose any RGB or CMYK combination for a color in CorelDraw, so perhaps this will help. Other pointers from folks who are more graphically savvy are also welcome. Thanks, Pat --- Patrick J. Loll, Ph. D. (215) 762-7706 ProfessorFAX: (215) 762-4452 Department of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA pat.l...@drexel.edu - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Abhianv Verma Research Associate, Daggett Lab,
Re: [PyMOL] How to make the dashed line having more dots?
play with set dash_gap, 0.3 (or choose your value) cheers, Abhi On Tue, Mar 4, 2008 at 10:15 AM, JunJun Liu ljjl...@gmail.com wrote: Hello everybody, I want to make a picture on which two close atoms are connected by a dashed line. I use the distance command to make the dashed line. However, there's only one dot to compose the whole dashed line. Is there a way to make the dashed line having more dots? == What I want: Atom_A Atom_B What PyMol gives: Atom_A - Atom_B === One more question on the dashed line. Can I modify the dashed line properties, like making it stronger or more compact? Thanks! Junjun - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Abhianv Verma Research Associate, Daggett Lab,
Re: [PyMOL] Distance labels
set_name oldname, newname On Feb 12, 2008 2:48 PM, Toni Pizà servo...@gmail.com wrote: An object whose name begins with an underscore will not appear in the menu. Perfect! But how can I change the name of one name in the Names Panel? -- Two of the most famous products of Berkeley are LSD and Unix. I don't think that this is a coincidence. http://servomac.blogspot.com - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Abhianv Verma Research Associate, Daggett Lab, Benjamin Hall Interdisciplinary Research Building University of Washington Box 355013 Seattle, WA 98195-5013
Re: [PyMOL] algorithm for alignment
there is something on the menu, file-save-molecule after the alignment, choose the molecule you want to save and just save. pymol saves the pdb with new coordinates. cheers, Abhi On Jan 25, 2008 10:29 PM, Lu Lin l...@cs.hku.hk wrote: Hi Hally, Thank you for your reply! Could you tell me how to save the alignment result to a new .pdb file? Thanks again! Best, Linda Hally Shaffer wrote: Linda, To align two proteins, they have to have the same number of atoms. You can manipulate the pdb files to delete part of one protein or remove a small molecule ligand if need be. You will need to save the corrected pdb files to load for the alignment. Attached is a picture of two proteins I aligned (one is in the apo form and the other is the ligand-bound holo form of the protein). The major difference between the two is indicated in red. I had to load my two pdb files and then the ligand (rea) as a separate pdb file. The commands are below. load 1LBDm.pdb, 1LBD load 1FBYm.pdb, 1FBY load REA.pdb, rea align 1LBD, 1FBY Good luck, Hally -- Hally Shaffer Graduate Student Georgia Institute of Technology School of Chemistry and Biochemistry gth8...@mail.gatech.edu Quoting Lu Lin l...@cs.hku.hk: Hi all, Anyone know which algorithm PyMOL uses to align or super of two structures? Thanks a lot! Best, Linda - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] can we add mutations to existed crystal structure models?
use wizard-mutagenisis.. On Dec 19, 2007 5:43 PM, wang,guojun wangguojun2...@hotmail.com wrote: hi, everyone, I want to make an image to show some structual differences between wild-tye ribosomal protein S12 and mutant type in bacteria. Does anybody know how to substitute wt aa residue with mutant type in an published crystal structed? or it is a mission impossible using PyMol. Thanks a lot! best regards, wang Ph.D Microbial Function Lab National Food Research Institute Tsukuba, 305-8642, JAPAN Tel: 81-29-838-8124 -- 七件武器，七种完美 立刻体验！ http://get.live.cn - SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Abhianv Verma Research Associate, Daggett Lab, Benjamin Hall Interdisciplinary Research Building University of Washington Box 355013 Seattle, WA 98195-5013
Re: [PyMOL] sphere diameter
set sphere_scale should scale the spheres, but they should be proportionate and they are van der waal spheres I guess, so chlorine is smaller than soduim.. http://pt.chemicalstore.com/ 227 vs 175 pm for na and cl respecively. On Nov 26, 2007 4:15 PM, Dr. Mark Mayer may...@mail.nih.gov wrote: hello, Can't find anything about this in docs or in settings: Where are sphere diameter settings controlled for individual atomic species: I'm trying to make fig with ions and the sizes don't seem to be right - Cl too small and Na too big. Thanks -- Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Abhianv Verma Research Associate, Daggett Lab, Dept. of Medicinal Chemistry, University of Washington, Seattle, WA, 98195-7610 USA
Re: [PyMOL] sphere diameter
Okey, something wierd and I do not understand. I am attaching 2 pdb files and 2 png's from pymol. 3.pdb, 4.pdb, 3.png and 4.png. Now the only difference between 3 and 4 are in blank spaces. and the sphere radius change between the two pdb files. In one Na is bigger and in other Cl is .. any ideas??.. bug or feature!! On Nov 26, 2007 5:53 PM, Mayer, Mark (NIH/NICHD) [E] may...@mail.nih.gov wrote: Thanks Abhinav, No other posts yet; you are probably right that these are VDW values, but nice to know for sure, and also good to be able to change to ionic radii if desired. -Original Message- From: Abhinav Verma [mailto:abhinav1...@gmail.com] Sent: Mon 11/26/2007 7:35 PM To: Mayer, Mark (NIH/NICHD) [E] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] sphere diameter set sphere_scale should scale the spheres, but they should be proportionate and they are van der waal spheres I guess, so chlorine is smaller than soduim.. http://pt.chemicalstore.com/ 227 vs 175 pm for na and cl respecively. On Nov 26, 2007 4:15 PM, Dr. Mark Mayer may...@mail.nih.gov wrote: hello, Can't find anything about this in docs or in settings: Where are sphere diameter settings controlled for individual atomic species: I'm trying to make fig with ions and the sizes don't seem to be right - Cl too small and Na too big. Thanks -- Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Abhianv Verma Research Associate, Daggett Lab, Dept. of Medicinal Chemistry, University of Washington, Seattle, WA, 98195-7610 USA -- Abhianv Verma Research Associate, Daggett Lab, Dept. of Medicinal Chemistry, University of Washington, Seattle, WA, 98195-7610 USA 3.pdb Description: Protein Databank data 4.pdb Description: Protein Databank data attachment: 3.pngattachment: 4.png
Re: [PyMOL] Secondary structure coloring
there is set cartoon_highlight_color, color command to set the highlight color to grey or something, so you can use that to color the other side of the secondary structure. On 10/10/07, Omar Davulcu o...@mailer.sb.fsu.edu wrote: Hi everyone, I've noticed that in some PDB files, not all, when I attempt to color a piece of secondary structure, like a helix, only one side will be colored and the underside is grey. I've even noticed that if I load two different PDB files in the same session, one will color both sides and the other will only color one. Is there a setting that will allow for both sides of a segment of a cartoon diagram to be colored? Thanks! Omar - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Abhianv Verma Research Associate, Daggett Lab, Dept. of Medicinal Chemistry, University of Washington, Seattle, WA, 98195-7610 USA
Re: [PyMOL] PDB changed CONNECT records
AFAIK setting connect_mode=1 strictly uses the CONECT records from pdb file to draw bonds. Cheers, Abhi. On 9/6/07, Mark A Saper sa...@umich.edu wrote: This was previously discussed in an archived email but I can't find it right now. Does the setting connect_mode=0 use the CONECT records in the PDB file or not? I think it does. Apparently in pdb code 1ABE, the CONECT records were changed in a 2005 revision. Two alternate sugar conformations are now interconnected when using the current 1ABE. The old 1ABE (from 1993) seems fine. Should setting connect_mode to 0 before loading PDB fix it? I don't think it does. Thanks, Mark _ *Mark A. Saper, Ph.D.* Associate Professor of Biological Chemistry Biophysics, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Problem with using Zoom command difficulty moving molecule
Dear Nicole, I can orient and zoom with the newpdb file I downloaded from the pdb databank. (there was no attachment in your email for the old one, but it wast needed as the orient and zoom works) Atleast I cannot reproduce anything you mentioned. Abhi On 9/5/07, Nicole Lewis-Rogers nlewisrog...@yahoo.com wrote: Dear Warren and Tsjerk, Thank you for responding so quickly to my question. I'm not sure what the underlying OpenGL graphics are on my computer. However, I have changed nothing on my computer. I can open and look at both versions of the pdb file in PyMOL, look at them side-by-side, and they respond very differently. The problem is reproducible. I don't how to write scripts yet, but I can give you a list of what I do. I have attached the two files: Old1FOD.pdb ( the file that is easy to use) and 1FOD.pdb (the most recent version of the file from RCSB that is difficult to use). 1) I double click on the pdb file and it opens automatically in PyMOL 2) In the Menu: Display: Sequence: Sequence Mode: Residues 3) Highlight residue #1 4) (sele) choose show sticks 5) (sele) choose Action: Find: Polar Contacts: To any atoms 6) (sele) choose Action: Orient or Zoom If I use the older version of the pdb file, the residue is zoomed in and I can easily turn the whole molecule around 360 degrees. If I use the newer version of the pdb file, the residue is zoomed out I cannot zoom in unless I use the left mouse button, and I cannot turn the molecule around 360 degrees. Thank you for your assistance, Nicole Lewis-Rogers -- Looking for a deal? Find great prices on flights and hotelshttp://us.rd.yahoo.com/evt=47094/*http://farechase.yahoo.com/;_ylc=X3oDMTFicDJoNDllBF9TAzk3NDA3NTg5BHBvcwMxMwRzZWMDZ3JvdXBzBHNsawNlbWFpbC1uY20-with Yahoo! FareChase. - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Pymol 1.0 graphics bug
although maybe out of context (as I am talking about the older pymol 0.99rc6 on windows), but the same happens with windows 2003 server . If you do not touch anything, the screen keeps updating. On 8/30/07, DeLano Scientific del...@delsci.info wrote: Roger, This isn't so much a PyMOL bug as a flaky characteristic of OpenGL under Windows XP, which eventually stops updating the screen when an application like PyMOL attempts to draw continuously for a long period of time without relinquishing control back to the operating system event loop. PyMOL isn't actually frozen when this happens -- it continues to render and write out images. Windows simply isn't updating the screen. The problem doesn't exist on Windows 2k or Linux, but a very similar behavior occurs with MacPYMOL (but which can be worked around by dragging the MacPyMOL window). Eventually we'll rearchitect PyMOL's event loop so as to eliminate this annoyance. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Roger Rowlett Sent: Thursday, August 30, 2007 9:15 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol 1.0 graphics bug In Pymol 1.0, the pymol viewer freezes during an mpng command in progress if the mouse pointer is moved. (Windows XP XP2 only, using Intel chips and motherboard, Nvidia graphics card and driver) PNG files are written out properly, and viewer window becomes live again after completion of the mpng command. I have verified this on two different systems, one with an Intel DG945CC board and Pentium D 805 with Nvidia GeForce 7300S and another with an Intel DQ965FE board and Core Duo 2 E6600 with XFX GeForce 8600 GT graphics. Both machines have 2 Gbyte of RAM and the latest Nvidia drivers. This behavior cannot be duplicated in Linux FC6 using a Quadro 980XGL and a single core Pentium 4, also with 2 Gbyte of RAM. Anybody else notice this? Cheers, -- --- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] different color structure of frames
hi one of doing this would be, to load ur file and then type the follwing for i in range(200): cmd.mset(str(i),str(i)) cmd.mdo(1, color yellow) cmd.mdo(101, color red) mplay cheers, Abhi Abhinav Verma Postdoc, University of Washington, Seattle WA On 8/29/07, Nicola Giacchè nico...@chimfarm.unipg.it wrote: Hi, it is possible to have frames with different colors of pdb structure? for example from 1 to 100 frames the structure must be yellow whereas from 101 to 200 the structure must be red... thanks, Nicola -- Nicola Giacchè, PhD Student Bachelor Degree in Medicinal Chemistry and Technology of Drugs University of Perugia Department of Medicinal Chemistry and Technology of Drugs Via del Liceo, 1 - 06123 Perugia (Italy) Tel ++39 075 585 5169/5156 E-mail: nico...@chimfarm.unipg.it - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] aligning multimodel pdb file
I want to align different models of a multimodel pdb file. How can I do that without extracting models as identical pdb. cheers, Abhi
Re: [PyMOL] selecting Na+ in pymol
Hi Warren Tsjerk, Thanks a lot for the explaination select r. na\+ did work for me (Pymol 0.99rc6 on Suse 10.1) cheers, Abhi. On 2/2/07, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Warren, Actually, I tried to use select .., r. na\+ as the second option, but that didn't work for me (Pymol 0.99b on Suse 9.2). Oh, and I owe you an elaborate answer still on the mail from a while ago. But that got a bit buried.. sorry ;) Tsjerk On 2/2/07, DeLano Scientific del...@delsci.info wrote: Tsjerk Abhinav, Actually, it was a bit surprising to me to see you're right. + is the default list separator in selections. For example: select posi, ARG+HIS+LYS/ select backbone, n. N+CA+C+O That is why it needs to be escaped with a backslash. Commas can also be used, but only within parentheses -- otherwise the parser gets confused, since commas are also used to separate command arguments. select backbone, (n. N,CA,C,O) Also, be aware when using backslashes inside a Python string that they are also a string escape character, so it is best to use two of them \\+. However, a single slash happens to work in this case for some bizzare reason. In other words, the PyMOL command: select selectionname, r. na\+ has a true Python equivalent of cmd.select(selectionname,r. na\\+) not cmd.select(selectionname,r. na\+) which actually works, but probably shouldn't. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Tsjerk Wassenaar Sent: Friday, February 02, 2007 2:23 AM To: Abhinav Verma Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] selecting Na+ in pymol Hi Abhi, Actually, it was a bit surprising to me to see you're right. Now, for showing/hiding, it has been dealt with in the code, by allowing the + to be left out. However, for selecting (and alter_ing) that doesn't go, apparently. A workaround is to use cmd.select(selectionname,r. na\+) or cmd.select(selectionname,n. na\+) Alternatively, you can change the residue/atomnames using: cmd.alter(r. na\+,resn='Na') or cmd.alter(n. na\+,name='Na') All of these worked for me. Of course, it would be good to have this dealt with properly in the same way as for showing/hiding. Hope it helps, Tsjerk On 2/2/07, Abhinav Verma abhinav1...@gmail.com wrote: Hallo, I have an annoying problem. I have pdb file with Na+ atoms defined as ATOM 1 Na+ Na+53 -1.106 7.854 52.244 1.00 0.00 Na now if want to select these Na+ with PyMOLselect n. na+ Selector: selection sele defined with 0 atoms. Any ideas how to select them? I tried renaming them to Na and then select n. na which works. So I assume the problem is + which is used for add in pymol. I also tried n. na+ which did not work either. thanks in advance, Abhi. -- --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier. Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=1216 42 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier. Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057; dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
[PyMOL] selecting Na+ in pymol
Hallo, I have an annoying problem. I have pdb file with Na+ atoms defined as ATOM 1 Na+ Na+53 -1.106 7.854 52.244 1.00 0.00 Na ATOM 2 Na+ Na+54 -0.106 3.854 27.244 1.00 0.00 Na ATOM 3 Na+ Na+55 1.894 -6.146 62.244 1.00 0.00 Na ATOM 4 Na+ Na+56 8.894 -5.146 42.244 1.00 0.00 Na ATOM 5 Na+ Na+57 -4.106 4.854 13.244 1.00 0.00 Na ATOM 6 Na+ Na+58 -10.106 -6.146 42.244 1.00 0.00 Na ATOM 7 Na+ Na+59 -7.106 5.854 35.244 1.00 0.00 Na ATOM 8 Na+ Na+60 4.894 4.854 49.244 1.00 0.00 Na ATOM 9 Na+ Na+61 9.894 -3.146 22.244 1.00 0.00 Na now if want to select these Na+ with PyMOLselect n. na+ Selector: selection sele defined with 0 atoms. Any ideas how to select them? I tried renaming them to Na and then select n. na which works. So I assume the problem is + which is used for add in pymol. I also tried n. na+ which did not work either. thanks in advance, Abhi.
Re: [PyMOL] set_dihedral command
1CRN for example has disulphide bonds which are covalant and thats why set_dihedral does not work. I think its the bug, which tells you that it has been setted to zero. So you have to remove the disulphide bonds before setting the dihedral angles. you can do so by unbond r. cys and n. sg, r. cys and n. sg and then PyMOLset_dihedral 21/n, 21/ca, 21/c, 22/n, 0.0 SetDihedral: adjusted to 0.000 PyMOLget_dihedral 21/n, 21/ca, 21/c, 22/n cmd.get_dihedral: -0.000 degrees. cheers, Abhinav. On 11/13/06, Chris Weichenberger cwe...@cosy.sbg.ac.at wrote: Dear PyMol users, I am trying to set dihedral angles in a protein. Unfortunately, the set_dihedral command is not documented, but it looks like it is the same as the get_dihedral with an additional value for the angle to set. I tried to set the dihedral angle for the protein crambin (PDB code 1CRN). First I query the angle: PyMOLget_dihedral 21/n, 21/ca, 21/c, 22/n cmd.get_dihedral: 136.344 degrees. I then assume that this command sets the dihedral angle to 0: PyMOLset_dihedral 21/n, 21/ca, 21/c, 22/n, 0.0 SetDihedral: adjusted to 0.000 Therefore, it should be the case that the angle is 0, however, it is still the old value: PyMOLget_dihedral 21/n, 21/ca, 21/c, 22/n cmd.get_dihedral: 136.344 degrees. The graphics has changed but the molecule's overall topology still looks like the original one. Also, repeating the above set_dihedral command results in successively altered graphics, which contradicts my inuition that setting a dihedral angle to the same fixed value should not result in any changes at all. Has anyone played around with this command and can report its proper usage? My ultimate goal is to write an animation that folds a protein from a more or less linear chain to its final correct 3D structure by interpolating dihedral angles. I am running PyMol version 0.97. Thanks for any help on this topic. _X - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] disulphide bonds in pymol
Hello, pymol finds the disulphide bonds very nicely when you load a pdb file. What I want is, to tell him not to do that. I need it for the fact that I need to set new values of dihedrals to the protein, and if there is a disulphide bond, then pymol just doesnt set the dihedrals. One way is to load the pdb file, then go to builder mode and then manually break the bond. and then execute the set dihedral command. But I wish to script it, so that I dont have to do it manually. Is there a way to do this, either putting builder commands in .pml scripts, or setting certain values, so that pymol doesnt look for sulphers. Thanks in advance, Abhi
