Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

Hi I think I'd say there was no hard way to do it either, before that stage (of course, I woudn't want to be too dogmatic about that, because that would be entirely out of character ;-). On 9 Sep 2009, at 21:09, Rafael Couñago wrote: Thanks for all the replies. I guess there's no easy

Re: [ccp4bb] ctruncate

Dear Ricardo Under certain circumstances, such as ice rings in the data, older versions of ctruncate can fail to output structure factors. The solution is to use a later version (1.0.02) of ctruncate, as distributed with CCP4-6.1.2. Norman -Original Message- From: CCP4 bulletin board

[ccp4bb] sorry

Oh dear - Apologies. I sent the ctruncate filre to the whole BB - maybe you SHOULD all update the distributed one from 6.1.1 but I didnt mean to do it that way.. Eleanor

[ccp4bb] Akta FPLC interface card

If anyone should have CU-900 interface card (unicorn communication) from a Akta FPLC system laying around they do not use anymore, we would be interested in buying it. Sorry for being off topic. Regards Michael -- Professor Michael Gajhede Institute of Medicinal Chemistry University of Copenhagen

[ccp4bb] side-topic: C-terminal protein sequencing service

Dear all, Does anyone know of a C-terminal sequencing service for proteins? Preferably one where one can simply send a blot to by normal mail. Apparently, here in Spain, there is none. Greetings, Mark Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia Universidad de Santiago 15782

[ccp4bb] Stacked Plate Like Crystals

Hello All, I have some plate crystals that are stacked to each other. They are about 60X50 micron. What are some methods that I can use to optimize them. Thank you all for the suggestions. Mariah -- Mariah Jones Department of Biochemistry University of Florida

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

Given some of the news reports about the testing of TSA in the US I would say you might have a good chance of getting the bomb on the plane. Now if you want more then 3 oz. of mouthwash you could be in trouble. Leonard Thomas lmtho...@ou.edu On Sep 9, 2009, at 6:18 PM, Ezra Peisach

[ccp4bb] Refinement of covalent ligand in Refmac5

Hello! I have an FAD cofactor that appears to be covalently bound to the Asp side chain (~1.6 A away). I was told that I need to refine the structure after indicating the covalent linkage in the pdb. If I add a line in the pdb LINK and then refine in Refmac5, FAD gets all messed up

[ccp4bb] status of truncate vs ctruncate?

As of 6.1.2, is there a consensus about using ctruncate versus truncate (the fortran version)? Pete

[ccp4bb] r-factor does not reduce

Hi everyone I am new to solving crystal structures so apologies for the simple question I am solving a structure using molecular replacement. I have refined my structure with refmac however the R-factor and R-free do not seem to go down with successive rounds of refinement. The initial

Re: [ccp4bb] r-factor does not reduce

Hello Sylvia, Two issues I would consider: 1) recheck the space group 2) make sure that I had selected a good model for my MR search All the Best, Sean

Re: [ccp4bb] r-factor does not reduce

It would not necessarily be unusual for an initial MR solution to have an R-factor of 45-48%, depending on the MR program used and quality of the search model. However, after an initial restrained refinement in Refmac, a good solution should drop pretty smartly from there. Some issues to

Re: [ccp4bb] r-factor does not reduce

On 09/10/2009 12:17 PM, Sean Seaver wrote: Hello Sylvia, Two issues I would consider: 1) recheck the space group 2) make sure that I had selected a good model for my MR search All the Best, Sean Hi Sylvia, If you have just used rigid body refinement - the Rfactor might be high until

[ccp4bb] non-CCP4 related: HKL2MAP availabilty

Hi everyone, Sorry for a non-CCP4 related question. I was looking for the program HKL2MAP for running SHELX from GUI. However my attempts to send mail to Tom Shneider did not work and bounced back. Can anyone please help me? Ajit B.

Re: [ccp4bb] r-factor does not reduce

Hi Sylvia, although modern MR programs perform rigid body refinement, it may be worth of giving a try a novel rigid body refinement protocol implemented in phenix.refine (MZ rigid-body refinement protocol), that has very high convergence radius: J. Appl. Cryst. (2009). 42, 607-615. "Automatic

Re: [ccp4bb] non-CCP4 related: HKL2MAP availabilty

Try thomas.schnei...@embl-hamburg.de - maybe you were spelling his name wrongly? George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Thu, 10 Sep 2009, Ajit

Re: [ccp4bb] non-CCP4 related: HKL2MAP availabilty

You can get hkl2map through a web interface, http://webapps.embl-hamburg.de/hkl2map/hkl2map_download.php Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 10 Sep 2009, Ajit Datta wrote: Hi everyone, Sorry for a non-CCP4

Re: [ccp4bb] r-factor does not reduce

On 10 Sep 2009, at 19:29, Pavel Afonine wrote: Hi Sylvia, although modern MR programs perform rigid body refinement, it may be worth of giving a try a novel rigid body refinement protocol implemented in phenix.refine (MZ rigid-body refinement protocol), that has very high convergence

Re: [ccp4bb] Refinement of covalent ligand in Refmac5

I believe you could try treating this Asp residue as an unnatural amino acid (FAD-Asp), and refine your structure with it. Peter Date: Thu, 10 Sep 2009 15:27:58 +0100 From: kpodzelin...@gmail.com Subject: [ccp4bb] Refinement of covalent ligand in Refmac5 To: CCP4BB@JISCMAIL.AC.UK Hello!

Re: [ccp4bb] Stacked Plate Like Crystals

You may be able to optimize them but that is still a step further, with recent advances in microbeam at the synchrotron, you *may* be able to scan through different regions of your crystal (especially if the stacking is not exactly one on top and is little oblique) and collect data! -- Karthik