[PyMOL] Finding coordinates of cgo object in Pymol
Hi All, I'd like to be able to find the coordinates of a cgo object on the pymol screen. Here's my workflow: 1. I generate a cgo object (a criss-cross) at a defined coordinate, and then drag it to a new coordinate. 2. I'd like to find the xyz coordinates of the new location. Could anyone tell me the commands needed to query the new location of the center of the crisscross? Thanks! and all the best, --Buz -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ 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
[PyMOL] Alignment Problems
Hi All, I'm having some trouble fitting to sets of residues in Pymol (1.2r0 - installed with Fink on MacOSX 10.5.8). I'm also having almost identical trouble using MacPymol as well (the version based on Pymol 1.1). I'm trying to align 2 sets of 4 cysteine residues. I have tried align, super and cealign. In each case, pymol fails to align the selections. Here is a sample of the error output: PyMOLalign Fam2_36169_Catalytic_Cys, CpI_Catalytic_Cys Match: read scoring matrix. Match: assigning 4 x 4 pairwise scores. MatchAlign: aligning residues (4 vs 4)... ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?). Alternatively; PyMOLsuper Fam2_36169_Catalytic_Cys, CpI_Catalytic_Cys MatchAlign: aligning residues (4 vs 4)... ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?). Could anyone help me with a workaround to this problem? 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] homology modeling in python
Hi Marcus, Thanks for your advice. I actually discovered Bizkit independently, and it definitely seems to fit the bill. Thanks for your advice! and all the best, --Buz On Jun 30, 2009, at 9:41 PM, Marcus Collins wrote: Hi Buz (and everyone) The biopython package together with Bizkit (http:// biskit.pasteur.fr/) claim to be able to do this sort of thing (see: http://biskit.pasteur.fr/use/workflows/homology-modelling) , and will chew up your processor rather than someone else's! Marcus Collins - Marcus D. Collins NIH NRSA Postdoctoral Fellow Departments of Physics and Chemistry University of Washington -- ___ 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] Homology Modeling in Pymol
Hi All, I have a very large library (almost 1000) of similar genetic sequences, for which I would like to generate homology models. Does anyone know of a way to automate requests to a homology modeling server, such as SWISS-Model through pymol, or alternatively through python? Thanks! and all the best, --Buz -- ___ 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] Mutating an Ion in Pymol and Displaying van der waals Radii
Thanks Warren! That worked really well. All the best, --Buz On Dec 18, 2008, at 10:08 PM, DeLano Scientific wrote: Buz, alter elem Na, elem='K' iterate elem K, print vdw show spheres, elem K alter elem K, vdw=1.4 rebuild iterate elem K, print vdw color yellow, elem K Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Buz Barstow [mailto:b...@mac.com] Sent: Thursday, December 18, 2008 2:30 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Mutating an Ion in Pymol and Displaying van der waals Radii Dear All, I'd like to mutate an ion in pymol from a potassium to a sodium. Is there an easy way to do this from the command line without having to edit the pdb file of the structure? Also, when one displays an atom (for instance a K atom) using the spheres representation, is the radius of the sphere equal to the Pauling radius of the atom (under the assumption that it is ionized)? For K, it looks like it is. Thanks! and all the best, --Buz -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009 .visitmix.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Mutating an Ion in Pymol and Displaying van der waals Radii
Dear All, I'd like to mutate an ion in pymol from a potassium to a sodium. Is there an easy way to do this from the command line without having to edit the pdb file of the structure? Also, when one displays an atom (for instance a K atom) using the spheres representation, is the radius of the sphere equal to the Pauling radius of the atom (under the assumption that it is ionized)? For K, it looks like it is. Thanks! and all the best, --Buz
Re: [PyMOL] Ray Tracing A Protein Gallery
Dear All, Thanks for all your suggestions on ray tracing the protein gallery. In the end, I used several of the techniques suggested, and everything worked out really well! To summarize: 1. Use the grid_mode option (only available in the compiled from source pymols) 2. Make a fake .pdb that has the corners and centers of a 3D box to use for alignment 3. Use the set_view command to apply the same viewing matrix 4. Use the zoom command with a center and a distance specified. Also, the cealign package is really helpful for aligning and translating very dissimilar molecules. Thanks! and all the best, --Buz On Dec 16, 2008, at 4:05 PM, DeLano Scientific wrote: Hi Buz, You can use center as a selection name for input with zoom, along with a distance value. zoom center, distance e.g. # first, get the object you want in the center of the screen orient # then zoom the viewer by a fixed amount about the center point zoom center, 10 # you may also wish to move the clipping planes in/out to avoid cutting into any of the molecular representations: clip atoms, 4, selection=all # also, depending upon the application, you might want to disable perspective set orthoscopic # get rid of background pixels unset opaque_background # render ray # and save save struct001.png Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -Original Message- From: Buz Barstow [mailto:b...@mac.com] Sent: Monday, December 15, 2008 11:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Ray Tracing A Protein Gallery Dear All, I'm making a gallery of protein molecules for my PhD thesis. I'd like to find an automatic way to ensure that all of the ray traced images have the same scale. Is there an easy way to do this? Thanks! and all the best, --Buz -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009 .visitmix.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Ray Tracing A Protein Gallery
Dear All, I'm making a gallery of protein molecules for my PhD thesis. I'd like to find an automatic way to ensure that all of the ray traced images have the same scale. Is there an easy way to do this? Thanks! and all the best, --Buz
[PyMOL] Making Stereo Pair Graphics
Dear All, I'd like to make a stereo pair graphic using pymol. I'd like to know what is an appropriate size for each image in the pair, and what their separation should be. Thanks! and all the best, --Buz
Re: [PyMOL] Making Stereo Pair Graphics
Hi Carsten, That did the trick! Thank you! All the best, --Buz On Nov 24, 2008, at 3:10 PM, Schubert, Carsten [PRDUS] wrote: Buz your image size will automatically be limited by the separation of two equal points in the respective images, which should be ~62 mm apart. Let me know if you need more details. Carsten -Original Message- From: Buz Barstow [mailto:b...@mac.com] Sent: Monday, November 24, 2008 3:01 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Making Stereo Pair Graphics Dear All, I'd like to make a stereo pair graphic using pymol. I'd like to know what is an appropriate size for each image in the pair, and what their separation should be. Thanks! and all the best, --Buz - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Selecting Negative Residues
Dear All,
Does anyone know how to select residues with negative sequence numbers
in Pymol?
I have a protein molecule with two residues with negative sequence
numbers (-2 and -1). When I issue the command:
cmd.select('temp', 'resi -2 and name CA')
Pymol selects the alpha carbons of residues -2 to +2.
How can I tell Pymol that I don't want to select a range?
Thanks, and all the best,
--Buz
Re: [PyMOL] Selecting Negative Residues
Hi Warren,
Thanks! That did the trick.
All the best,
--Buz
On Aug 21, 2008, at 4:25 PM, DeLano Scientific wrote:
Buz,
This is something PyMOL didn't handle well until recently, but I
think you
can now prefix the minus sign with a backslash in order to force
PyMOL to
interpret the value numerically instead of as a range.
# create some negative residue identifiers
load $TUT/1hpv.pdb
alter chain A, resi=int(resi)-200
set seq_view
# test selections
indicate resi \-127
indicate resi \-136-\-129
A bit ugly, but it works!
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Buz
Barstow
Sent: Thursday, August 21, 2008 12:32 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Selecting Negative Residues
Dear All,
Does anyone know how to select residues with negative sequence
numbers in
Pymol?
I have a protein molecule with two residues with negative sequence
numbers
(-2 and -1). When I issue the command:
cmd.select('temp', 'resi -2 and name CA')
Pymol selects the alpha carbons of residues -2 to +2.
How can I tell Pymol that I don't want to select a range?
Thanks, and all the best,
--Buz
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK win great
prizes Grand prize is a trip for two to an Open Source event
anywhere in the
world http://moblin-contest.org/redirect.php?banner_id=100url=/
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[PyMOL] Graphics Workstation
Dear All, I'm considering purchasing a new graphics workstation for molecular graphics and macromolecular refinement. I'm considering buying a machine with 2 quad core xeon processors, and a nVidia Quadro FX graphics card with 1.5 Gb of memory. Can the current generation of software, and maybe the next generation of visualization software, make use of a system with so many processors, or am I better off spending the money elsewhere? Thanks! and all the best, --Buz
Re: [PyMOL] Pymol Crash in X11 on MacOSX 10.5
Hi William and Warren, I've also updated to OSX 10.5.2, and any issues that I had with Pymol seem to have been resolved, even when running under conditions that would previously have caused a crash. I'm going to keep my fingers crossed for now. Thanks! and all the best, --Buz On Feb 12, 2008, at 2:07 PM, William Scott wrote: I've noticed after updating to X11 2.1.3 that X11 crashes reproducibly if I (for example) resize coot's window before it finishes loading. I don't recall having X11 crash ever with 2.1.1 or earlier. Fortuitiously, the 10.5.2 update reverts X11 to 2.1.1, so updating that might solve the problem ... On Mon, 11 Feb 2008, Buz Barstow wrote: Hi All, I've been having a lot of trouble with Pymol since upgrading to the X11 included with MacOS 10.5. Of late (using X11 2.1.3), Pymol built with fink, and ipymol 1.0 have been crashing after a small amount of viewing and rotating an object in the program (a few rotations and zooms). Unfortunatley, after X11 crashes, it refuses to restart properly until the computer is restarted. Using the X11 pymol has been quite important to me, as I need to be able to use a number of python modules that I have downloaded with fink such as numpy and scipy, as well as some modules that I have written myself. Is there a way that I can make MacPymol aware of these modules? Thanks! and all the best, --Buz -- - 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
[PyMOL] Pymol Crash in X11 on MacOSX 10.5
Hi All, I've been having a lot of trouble with Pymol since upgrading to the X11 included with MacOS 10.5. Of late (using X11 2.1.3), Pymol built with fink, and ipymol 1.0 have been crashing after a small amount of viewing and rotating an object in the program (a few rotations and zooms). Unfortunatley, after X11 crashes, it refuses to restart properly until the computer is restarted. Using the X11 pymol has been quite important to me, as I need to be able to use a number of python modules that I have downloaded with fink such as numpy and scipy, as well as some modules that I have written myself. Is there a way that I can make MacPymol aware of these modules? Thanks! and all the best, --Buz
[PyMOL] MSMS Cavity Visualization in Pymol
Hi All, Does anyone know of a script that is capable of displaying the surfaces identified by msms in pymol? It would be nice to have a program that could read in existing .vert and .face files. I've included small starting sections of these .face and .vert files as examples: # MSMS solvent excluded surface vertices for protein.xyzr #vertex #sphere density probe_r 2821296 1.00 1.20 26.022 6.472 7.936-0.226 0.027-0.974 0 607 2 24.564 6.680 6.807 0.989-0.147-0.033 0 655 2 25.071 7.472 6.969 0.567-0.807-0.168 0 657 2 24.499 6.386 6.838 0.956-0.293-0.018 0 655 2 25.956 6.178 7.966-0.259-0.120-0.958 0 607 2 25.398 5.470 7.845 0.206 0.471-0.858 0 608 2 25.738 5.204 7.835 0.376 0.338-0.863 0 608 2 # MSMS solvent excluded surface faces for protein.xyzr #faces #sphere density probe_r 5601296 1.00 1.20 1 5195 3 3 195 5196 3 3 195196 2 3 3 2196 4 3 3 5 8 6 3 5 6 8 7 3 5 8 11 9 3 7 9 11 10 3 7 Thanks! and all the best, --Buz
Re: [PyMOL] Algorithm to Rotate One Set of Vectors onto Another
Hi Jason, Thanks a lot for this! I was able to code up a very simple solution to my problem using Tsjerk's suggestion. In my problem I have a series of very similar structures, and I wanted to calculate the principal axes of a section of these structures and then align the principal axes of another section of the structure with those principal axes: while i len(eigVectors0001_1): # the m matrix is a matrix of the principal axes of segment 1 of structure 1 m = array([eigVectors0001_1[1], eigVectors0001_2[1], eigVectors0001_3[1]]) m = transpose(m) # The n matrix is a matrix of the principal axes of segment of structure i n = array([eigVectors0001_1[i], eigVectors0001_2[i], eigVectors0001_3[i]]) n = transpose(n) # r is the rotation matrix to rotate the n axes onto the m axes r = dot(m,inverse(n)) # p is a matrix of the principal axes of segment 2 in structure i p = array([eigVectors0002_1[i], eigVectors0002_2[i], eigVectors0002_3[i]]) p = transpose(p) # q are the rotated principal axes of segment 2 in structure i q = dot(r,p) i+=1 Thanks again! and all the best, --Buz On Jan 29, 2008, at 8:31 AM, Jason Vertrees wrote: Buz, Tsjerk's answer is right on. This has already been implemented for PyMOL as a plugin. See Kabsch/optAlign from cealign, here: http://www.pymolwiki.org/index.php/Kabsch The code is open-source and so can be applied elsewhere. Another simple method is to simply calculate the SVD of the correlation matrix. Then multiply the right and left singular vectors by each other -- that will yield the DxD rotation matrix (where D is the dimension of your vector sets). (This is how Kabsch/optAlign works.) -- Jason On Monday 28 January 2008 10:48:29 pm pymol-users-requ...@lists.sourceforge.net wrote: -- Message: 3 Date: Sat, 26 Jan 2008 10:04:06 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [PyMOL] Algorithm to Rotate One Set of Vectors onto Another To: Buz Barstow b...@mac.com Cc: pymol-users@lists.sourceforge.net Message-ID: 8ff898150801260104k4902e5f0tcb94e8ebbbf1e...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Buz, To my opinion, this is not the best place for your question. Pymol is a molecular viewer... But the question itself is basically trivial from the linear algebra point of view. If X is your source set of orthogonal vectors and Y is the target, then you should have some sort of matrix R to satisfy Y = RX But, since it should only be a rotation, you'll first have to transform X and Y to their orthonormal counterparts N and M: M = RN Then MN^-1=RNN^-1 such that R = MN^-1 If both sets are of equal dimensions (and full rank), there's an exact solution. Otherwise, there's a bit more trouble... So, taking your favourite language with the proper linear algebra package, it comes down to: normalize X - N normalize Y - M invert N multiply M with the inverse of N By the way, you're probably dealing with 3x3 matrices here (molecules in cartesian space), in which case the routines are simple enough to write down yourself (I believe these were even in the array.py I posted like two days ago). Hope it helps, Tsjerk On Jan 25, 2008 10:55 PM, Buz Barstow b...@mac.com wrote: Dear All, I'm looking for an algorithm that will allow me to derive a transformation matrix that superimposes one set of orthogonal vectors onto another set of orthogonal vectors, that I can then use to transform another set of orthogonal vectors. Thanks! and all the best, --Buz -- Jason Vertrees (javer...@utmb.edu) Doctoral Candidate Biophysical, Structural Computational Biology Program University of Texas Medical Branch Galveston, Texas http://www.best.utmb.edu/ http://www.pymolwiki.org/ - 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
[PyMOL] Algorithm to Rotate One Set of Vectors onto Another
Dear All, I'm looking for an algorithm that will allow me to derive a transformation matrix that superimposes one set of orthogonal vectors onto another set of orthogonal vectors, that I can then use to transform another set of orthogonal vectors. Thanks! and all the best, --Buz
[PyMOL] Rigimol Output
Dear All, Does anyone know the exact meaning of the output from the first rigimol processing step? For instance, if I give the rigimol program two structures that are very similar (structure #1 and structure #2), the program identifies several domains and gives the following output: Rotations and Translations Domain RMSD Axis Angle Translation Distance 1 0.19 ( 0.17, 0.26, 0.91) -0.00 ( 0.00,-0.00,-0.00) 0.00 2 0.17 (-0.65, 0.13, 0.74)0.35 ( 0.04, 0.06,-0.03) 0.08 3 0.21 ( 0.33, 0.33, 0.82) -0.19 (-0.03,-0.03,-0.04) 0.06 4 0.20 ( 0.49, 0.41, 0.61)0.27 (-0.02, 0.02,-0.06) 0.06 5 0.14 ( 0.40, 0.04, 0.92) 16.41 (-0.74, 0.36, 0.20) 0.85 6 0.20 (-0.51,-0.47, 0.48) 23.92 (-0.39,-0.09,-1.21) 1.27 7 0.51 ( 0.61,-0.15, 0.82) -67.57 ( 1.27, 0.40,-0.49) 1.42 8 0.04 ( 0.11,-0.14, 0.99) 113.72 ( 0.58,-0.07,-0.09) 0.59 9 0.11 ( 0.02, 0.36, 0.85) -65.37 (-0.28, 0.80,-0.62) 1.05 10 0.05 (-0.67, 0.55, 0.36) 48.20 (-0.44,-1.14,-0.26) 1.25 11 0.41 ( 0.73, 0.13, 0.85) -88.51 (-0.22, 0.13,-0.11) 0.28 12 0.02 (-0.17, 0.88,-0.39) -131.04 ( 0.07,-0.42,-0.43) 0.60 13 0.02 (-0.46, 0.96,-0.05) -86.21 ( 0.07, 0.03,-0.92) 0.92 14 0.00 (-0.74, 0.23, 0.76) -111.08 (-1.16, 1.00,-0.61) 1.65 1. How meaningful is this output, if you'll excuse the rather vague question? 2. On a related thought, what exactly do the columns in the output mean? I can imagine that the RMSD is the root mean square deviation between domain 1 in structure #1 and domain 1 in structure #2. 3. What is the Axis column, and how is the axis defined? Also, what about the angle, and how is it defined? Is it the rotation of the domain about that axis from structure #1 to #2? 4. I'm guessing that the translation column gives the translation vector of the center (maybe center of mass) of the domain from structure #1 to #2. Am I right, and is the center the center of mass? Thanks! and all the best, --Buz
[PyMOL] Principal axes and moment of inertia matrix
Dear All, Does anyone have a python routine that can be used to calculate the moment of inertia matrix, and principal axes of a collection atoms? Thanks! and all the best, --Buz
[PyMOL] Calculation of Domain Volume in Pymol
Dear all, I'd like to very accurately calculate the volume of a selection in pymol, or with tools that are callable by pymol? Could anyone suggest a program or algorithm? Thanks! and all the best, --Buz
[PyMOL] Adding Hydrogens to GFP Chromophore
Hi all, I'm trying to use PyMol to add hydrogen atoms to this small fragment of a PDB file, the chromophore from the GFP structure 1EMA; REMARK S65T Chromophore from Ormo's coordintes (1EMB). HETATM 466 N1 CRO66 24.077 27.513 36.610 1.00 11.86 N HETATM 467 CA1 CRO66 25.011 26.478 37.078 1.00 7.34 C HETATM 468 CB1 CRO66 25.931 26.035 35.930 1.00 10.77 C HETATM 469 CG1 CRO66 25.155 25.422 34.796 1.00 16.67 C HETATM 470 OG1 CRO66 26.679 27.129 35.461 1.00 14.22 O HETATM 471 C1 CRO66 25.730 27.106 38.245 1.00 18.38 C HETATM 472 N2 CRO66 26.975 27.732 38.216 1.00 9.21 N HETATM 473 N3 CRO66 25.274 27.124 39.509 1.00 17.10 N HETATM 474 C2 CRO66 26.043 27.875 40.370 1.00 5.46 C HETATM 475 O2 CRO66 26.022 27.962 41.566 1.00 13.20 O HETATM 476 CA2 CRO66 27.197 28.245 39.512 1.00 16.08 C HETATM 477 CA3 CRO66 23.919 26.721 39.842 1.00 10.87 C HETATM 478 C3 CRO66 23.745 25.326 40.360 1.00 19.28 C HETATM 479 O3 CRO66 22.885 25.116 41.193 1.00 15.72 O HETATM 480 CB2 CRO66 28.329 28.822 39.960 1.00 10.75 C HETATM 481 CG2 CRO66 29.437 29.370 39.124 1.00 7.67 C HETATM 482 CD1 CRO66 29.541 29.103 37.742 1.00 11.31 C HETATM 483 CD2 CRO66 30.487 30.110 39.805 1.00 10.79 C HETATM 484 CE1 CRO66 30.707 29.546 37.033 1.00 17.44 C HETATM 485 CE2 CRO66 31.614 30.563 39.085 1.00 10.01 C HETATM 486 CZ CRO66 31.718 30.300 37.721 1.00 9.48 C HETATM 487 OH CRO66 32.894 30.804 36.971 1.00 13.84 O CONECT 466 457 467 CONECT 467 466 468 471 CONECT 468 467 469 470 CONECT 469 468 CONECT 470 468 CONECT 471 467 472 473 CONECT 472 471 476 CONECT 473 471 474 477 CONECT 474 473 475 476 CONECT 475 474 CONECT 476 472 474 480 CONECT 477 473 478 CONECT 478 477 479 488 CONECT 479 478 CONECT 480 476 481 CONECT 481 480 482 483 CONECT 482 481 484 CONECT 483 481 485 CONECT 484 482 486 CONECT 485 483 486 CONECT 486 484 485 487 CONECT 487 486 END Unfortunately, PyMol adds too many hydrogens to each carbon in the tyrosine ring in the center of the chromophore. It doesn't recognize that some of the carbons can have double bonds. Does anyone know the best way to get PyMol to recognize the double bonds? All the best, --Buz |-| Buz Barstow 192 Clark Hall Cornell University Ithaca, NY 14853, USA Email: b...@cornell.edu Phone: 607 255 8678 Fax: 607 255 8751 |-|
[PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
Hi, I've been using Pymol 0.93 on SuSE Linux 8.2 for a few hours now, and I'm having trouble ray tracing graphics. I installed Pymol from the source file pymol-0_93-src.tgz. Each time I start the ray tracer Pymol quits with a segmentation fault error; /usr/local/pymol/pymol.com: line 2: 29720 Segmentation fault /usr/bin/python /usr/lib/python2.2/site-packages/pymol/__init__.py $* I've tried setting max_threads to 1, and this doesn't resolve the problem. I've also downloaded the patch for glibc from SuSE and this doesn't help the problem either. Can anyone help? Best, --Buz |-| Buz Barstow 192 Clark Hall Cornell University Ithaca, NY 14853, USA Email: b...@cornell.edu Phone: 607 255 8678 Fax: 607 255 8751 |-|
