[ccp4bb] Real space refinement in coot

Anyone know how to minimize the domination of heavy atoms during RSR in coot. The density from my zincs causes the coordinating His residues to collapse onto the metal ion when I try RSR. Cheers in advance Dean

Re: [ccp4bb] How to make covalent bond in COOT

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Saugata, if you want coot to refine the bond length, you have to rename the residue to some name coot does not yet understand and create a cif-file which includes the restraints of the residue, the ligand, and the bond between the two. Tim On

Re: [ccp4bb] How to make covalent bond in COOT

On 07/12/11 09:47, Tim Gruene wrote: if you want coot to refine the bond length, you have to rename the residue to some name coot does not yet understand and create a cif-file which includes the restraints of the residue, the ligand, and the bond between the two. JLigand is the way to do

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[ccp4bb] Fwd: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?

-- Forwarded message -- From: 商元 shangyuan5...@gmail.com Date: Wed, Dec 7, 2011 at 6:41 PM Subject: Re: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server? To: Jose Duarte jose.dua...@psi.ch Dear Jose, Thanks for you kind replies

Re: [ccp4bb] How to make covalent bond in COOT

On 7 Dec 2011, at 10:08, Paul Emsley wrote: On 07/12/11 09:47, Tim Gruene wrote: if you want coot to refine the bond length, you have to rename the residue to some name coot does not yet understand and create a cif-file which includes the restraints of the residue, the ligand, and the bond

Re: [ccp4bb] How to make covalent bond in COOT

I think you are probably asking the wrong question, and what you are eventually going to want to know is how do I get a modified amino acid recognized in PHENIX or REFMAC so that it makes proper peptide bonds. The making and breaking of bonds in COOT (or O for ligands) is not something that

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Re: [ccp4bb] Fwd: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?

Then probably PFAM does what you want http://pfam.sanger.ac.uk Best Jose On 12/07/2011 11:43 AM, 商元 wrote: -- Forwarded message -- From: *商元* shangyuan5...@gmail.com mailto:shangyuan5...@gmail.com Date: Wed, Dec 7, 2011 at 6:41 PM Subject: Re: [ccp4bb] Did anyone here know

Re: [ccp4bb] How to make covalent bond in COOT

Oops, Meant to hit reply all... Hi there, You can generate a link via jligand which gives you a covalent linkage with your enzyme / ligand.as well as a cif file Try the tutorial ftp://ftp.ccp4.ac.uk/JLigand/tutorial_link.html J _ Joel Tyndall, PhD Senior

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Re: [ccp4bb] How to make covalent bond in COOT

On 07/12/11 11:58, matthew vetting wrote: I think you are probably asking the wrong question, and what you are eventually going to want to know is how do I get a modified amino acid recognized in PHENIX or REFMAC so that it makes proper peptide bonds. The making and breaking of bonds in COOT

[ccp4bb] OSX and stereo

Can anyone positively confirm that the new Zalman monitors M240W or M215W actually work on macs and pymol/coot? Specifically, I want to put this on a new macpro with an ATI Radeon HD 5770 card, but we also have older systems. Answers are very much appreciated, thanks in advance. Erik

Re: [ccp4bb] OSX and stereo

On Wed, Dec 7, 2011 at 3:48 PM, Erik Martinez-Hackert e...@cns.msu.edu wrote: Can anyone positively confirm that the new Zalman monitors M240W or M215W actually work on macs and pymol/coot? Specifically, I want to put this on a new macpro with an ATI Radeon HD 5770 card, but we also have

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Re: [ccp4bb] OSX and stereo

Yep - works fine on Coot and Chimera. Others may correct me, but I don't think Schrodinger have re-instated support in PyMol? I use it daily - the Zalman is the primary monitor on my desk. The great advantage of this type of monitor (IMHO) is that it is hardware independent.

Re: [ccp4bb] OSX and stereo

Works fine with MacPyMOL v. 1.5. You have to copy MacPyMOL.app to MacPyMOLZalman.app and fire this off. Cheers, Scott Scott T. R. Walsh, Ph.D. Assistant Professor University of Maryland College Park Institute for Bioscience and Biotechnology

[ccp4bb] Efficient way of showing residue conservation

I once saw a figure showing the protein as surface, but instead of having it coloured by atom type or potential, it was shown by percent conservation in the family. Something like red highly conserved, all the way to white, not conserved at all... Now, I assume the figure was done by uploading

Re: [ccp4bb] Efficient way of showing residue conservation

Usually you put a statistic like this in the tempFactor field (B) and then color by B-factor in pymol or similar. I'm certain there is a facility for filling this entry somewhere. If not, then a fairly trivial server is waiting for someone to create it and claim the glory. Google something

Re: [ccp4bb] Efficient way of showing residue conservation

Consurf will do this for you. Bostjan --- Bostjan Kobe NHMRC Research Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper

[ccp4bb] model building at 3.2 A

Dear all I have crytals which diffract up to 3.2 A at synchrotron, I am solving this by molecular replacement. I have built 70% of the model successfully,but the problem is it have a very poor density for some 30-40 residues at N terminal. I can't build anything in this region,this could be

Re: [ccp4bb] model building at 3.2 A

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Atul, the resolution of your data set would affect the whole unit cell and not just the region of 30-40 residues. The more likely reason is a disordered N-terminus. There is nothing to do about this in silico. It may be worth recloning your