[ccp4bb] Map conversion
Dear all, Is any other program for map conversion other than MAPMAN? If so please tell me. Thanaks! Regards, Sampath
[ccp4bb] Phd studentship in structural biology and biophysics
A Phd studentship is available in the group of Prof. Remy Loris to work on the structural biology and biophysics of the MazEF toxin-antitoxin module from Staphylococcus aureus. The project centres around crystal structure determination of the MazEF module and its complexes, interaction studies using a variety of biophysical techniques and, in collaboration with Prof. Ambrose Cheung (Dartmouth Medical School, USA), the development of small molecule drugs that interfere with the interaction between MazE and MazF. Further information concerning bacterial toxin-antitoxin modules can be found in Buts et al. (2005) Toxin-antitoxin modules as bacterial metabolic stress managers. Trends Brioche. Sci. 30(12), 672-679. Enquiries can be send to Prof. Remy Loris ([EMAIL PROTECTED]). Please attach a recent CV and the names of at least two referents. Remy Loris Vrije Universiteit Brussel http://www.vib.be/ http://www.structuralbiology.be/
[ccp4bb] chromophore in GFP
Hi everybody, we have solved the X-ray structure of a GFP (green fluorescent protein) containing complex. During refinement of the structure we now encountered the problem of connecting the GFP chromophore covalently to the polypeptide chain. We introduced the chromophore to our model as a separate ligand with separate toplogy. So far we could not find a way to integrate it in the primary sequence. Any idea how this problem can be solved? Which programs might be useful? Thank you very much in advance. Best, Sheng Axel * Dr. Sheng CUI 崔胜 Department of Chemistry and Biochemistry Gene Center University of Munich Feodor-Lynen-Str. 25 81377 Munich, Germany Tel: +49 89 2180-76984 Fax: +49 89 2180-76999 e-mail: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] Web:http://www.lmb.uni-muenchen.de/hopfner/welcome.html http://www.lmb.uni-muenchen.de/hopfner/welcome.html ***
Re: [ccp4bb] sequential renumbering of a messed up pdb file
Dear Martin et al:
This, along with some scripting in coot and my favorite shell (zsh),
did the trick.
Many thanks to all who replied, and apologizes for what in retrospect
must have been a very poorly-worded question.
Maybe this functionality can be incorporated in the next release of
perlmole.
Bill Scott
On Jul 31, 2008, at 9:05 PM, Martin.Laurberg wrote:
Bill,
Almost there then (I wrote the line without checking)..
I moved the 'P' one position to the left and now it works, provided
first
atom record of every atom record is the phosphor (/ P /) atom :
perl -ne 'BEGIN{$i=0}if (/^ATOM/) \
{if (substr($_,12,4) =~ / P /){$i++}; \
substr($_,22,4,sprintf(%4.0f,$i))}{print}' file.pdb
On Thu, 31 Jul 2008, William G. Scott wrote:
turned them all to zeros
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Jul 31, 2008, at 5:03 PM, Martin.Laurberg wrote:
Bill, if each residue starts at the same atom name, something
close to
this might work:
perl -ne 'BEGIN{$i=0}if (/^ATOM/){if (substr($_,12,4) =~ / P /){$i+
+};
substr($_,22,4,sprintf(%4.0f,$i))}{print}' file.pdb
/Martin
--
Martin Laurberg, PhD
Noller Laboratory
225 Sinsheimer Laboratories
University of California at Santa Cruz
CA-95064 Santa Cruz
USA
Tel +1 (831) 459 35 84
Fax +1 (831) 459 37 37
On Thu, 31 Jul 2008, William Scott wrote:
Hi folks:
I am hoping there is a simple answer I have overlooked to the
following question. I have a pdb file in it that has multiple
residues that have the same number and chain ID, and I want to
force
them to be renumbered sequentially. Is there a simple way to do so
(eg, pdbset) or am I doomed to fixing it manually?
Thanks.
Bill Scott
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
[ccp4bb] Pymol movie ration along any axis
Hi , all: Sorry for this off-topic question. When you make movies, Pymol usually allows you rotate molecules along x, y, or z axis. The view point is always from Z axis. Does anyone have this experience of rotating molecules along any other specified axis and keeping the same view point as usual? Thanks a lot. Jerry _ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_video_072008
Re: [ccp4bb] Pymol movie ration along any axis
Jerry said: Does anyone have this experience of rotating molecules along any other specified axis and keeping the same view point as usual? I have, but its complicated. (Interpolated) rotation about an arbitrary axis is not a straightforward operation, especially if said axis does not pass through the origin. You are well advised to describe your rotation as a quaternion transformation, calculate the interpolations in quaternion space, convert them to the pymol transformation matrices (which are not conventional transformation matrices) and apply those, saving frames as you go. But you can have a lot of fun figuring out how to do it if you can spare the time. It may be a simpler process these days though. That was a couple of years ago. James On Aug 1, 2008, at 2:06 PM, Jerry McCully wrote: Hi , all: Sorry for this off-topic question. When you make movies, Pymol usually allows you rotate molecules along x, y, or z axis. The view point is always from Z axis. Does anyone have this experience of rotating molecules along any other specified axis and keeping the same view point as usual? Thanks a lot. Jerry -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com
Re: [ccp4bb] Pymol movie ration along any axis
You should also have a look at emovie http://www.weizmann.ac.il/ISPC/eMovie_download.html That gives you more flexibility, but if you really want to control things, then write a script which saves frames step by step as you turn your molecule in any direction you want. Jürgen On 1 Aug 2008, at 14:06, Jerry McCully wrote: Hi , all: Sorry for this off-topic question. When you make movies, Pymol usually allows you rotate molecules along x, y, or z axis. The view point is always from Z axis. Does anyone have this experience of rotating molecules along any other specified axis and keeping the same view point as usual? Thanks a lot. Jerry Use video conversation to talk face-to-face with Windows Live Messenger. Get started. - Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
Re: [ccp4bb] Pymol movie ration along any axis
I just realized a simplification wherein you can skip quaternions. My guess is you just want a rigid body to sit there and rotate without defined starting and ending orientations. Here is what you do: you decide how fast you want it to rotate, in terms of frames, then you figure out the rotation per frame. You can think of this as an incremental axis and angle rotation. Then you describe that increment as a 3x3 rotation matrix. This conversion is not that difficult. Scipy I think can do this without any thought from the programmer. This 3x3 rotation transformation can get plugged straight into the pymol transformation matrix. Then, between frames, you just keep applying that transformation and it will rotate dutifully. If the axis doesn't intersect the origin (e.g. your rigid body is not centered at the origin, etc) you apply the transformation to center it, apply the rotation, then move the rigid body back, then take the frame. Repeat. Probably such a thing would be trivial to add to emovie since its open sourced. The parameters would be (x0,y0,z0) and (x1,y1,z1) describing the arbitrary rotation axis, and d, describing the number of degrees to rotate per frame. The bigger the d, the faster. James On Aug 1, 2008, at 2:06 PM, Jerry McCully wrote: Hi , all: Sorry for this off-topic question. When you make movies, Pymol usually allows you rotate molecules along x, y, or z axis. The view point is always from Z axis. Does anyone have this experience of rotating molecules along any other specified axis and keeping the same view point as usual? Thanks a lot. Jerry Use video conversation to talk face-to-face with Windows Live Messenger. Get started. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com
Re: [ccp4bb] chromophore in GFP
Defining specific restraints on bonds connecting the chromophore with the rest of the protein worked fine for us in Refmac when we solved a turboGFP structure a couple of years ago. There wasn’t anything special that had to be done �C all strictly by the book… Artem _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of sheng CUI Sent: Friday, August 01, 2008 7:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] chromophore in GFP Hi everybody, we have solved the X-ray structure of a GFP (green fluorescent protein) containing complex. During refinement of the structure we now encountered the problem of connecting the GFP chromophore covalently to the polypeptide chain. We introduced the chromophore to our model as a separate ligand with separate toplogy. So far we could not find a way to integrate it in the primary sequence. Any idea how this problem can be solved? Which programs might be useful? Thank you very much in advance. Best, Sheng Axel * Dr. Sheng CUI 崔胜 Department of Chemistry and Biochemistry Gene Center University of Munich Feodor-Lynen-Str. 25 81377 Munich, Germany Tel: +49 89 2180-76984 Fax: +49 89 2180-76999 e-mail: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] Web:http://www.lmb.uni-muenchen.de/hopfner/welcome.html http://www.lmb.uni-muenchen.de/hopfner/welcome.html ***
Re: [ccp4bb] question about getting rid of model bias in refinement
Hello Eleanor, Thank you very much for your reply. I don't know whether or not the conformation is model biased or not. I just want to make sure the conformation is model free of model bias because these residues are important. The refinement moved the residue back may indicate the previous conformation is correct. I want to know whether there are any other methods to cross-verify the result. Thank you very much for your opinions. Best, Sun --- On Thu, 7/31/08, Eleanor Dodson [EMAIL PROTECTED] wrote: From: Eleanor Dodson [EMAIL PROTECTED] Subject: Re: [ccp4bb] question about getting rid of model bias in refinement To: [EMAIL PROTECTED] Date: Thursday, July 31, 2008, 11:41 AM Sun Tang wrote: Hello Everyone, I have a question about getting rid of model bias in refinement with refmac. I solved the structure with molecular replacement. After final refinement of the structure, I found out some key amino acids in the structure and wanted to make sure their conformations are correct. I omitted these amino acids (by setting occupancy to zero) and refined the structure. I manually fit the amino acids into the density and refined the structure again. I found these amino acids return to the precious conformations even though the conformations I fit were different. Should I omit these amino acids from the beginning of the refinement? What is the best way to get rid of the model bias? Your suggestions are greatly appreciated! Best, Sun This seems rather strange! The bias would usually disappear especially if you have a) set occs to 0.0 for selected residues, b) done several cycles of refinement. Could there be 2 conformations for these residues? One where it was originally and one where you have built them? Eleanor
