Re: [ccp4bb] xds undefined data_range error

Hello, I had a similar problem, maybe the same error message. I think, the line NAME_TEMPLATE_OF_DATA_FRAMES=?? should be as short as possible (48 characters or something). There was a limitation of number of characters (maybe fixed in newest versions of XDS). I would creat

Re: [ccp4bb] high number of lysines

Hello Amit, 1. You may have to dramatically increase your protein concentration to get into the crystallization range. What is the maximum solubility of your protein? What protein concentration are you currently working with? 2. Try the UCLA surface entropy reduction server (nihserver.m

Re: [ccp4bb] mtz2various is broken [ was: Another pointless question ]

On Tuesday 09 June 2009 02:45:41 Ian Tickle wrote: > > Ethan - that's odd it works for me (CCP4 6.1.0) unless of course it got > broken recently in 6.1.1: I see the same problem in both 6.0.2 and 6.1.1. I don't have a copy of 6.1.0 around to test. Your version fails to convert space group "4005"

Re: [ccp4bb] xds undefined data_range error

Hello, What is the actual data range at the particular line? Maybe you could append your XDS.INP to send it to the board for inspection? Did you really name the file XDS.inp? As far as I understand, xds will be looking for all upper case characters, so XDS.inp might not be read at all. Ar

[ccp4bb] CCP4 6.1.0 Balbes error

Dear BB Balbes (run from within CCP4i) gave me one MR solution but stopped with this error. I am now using the Balbes WWW server, but could some of you knowledgeable guys have some ideas of might be going on? Thanks Victor Alves Some info from log file: BALBES Version is 0.0.1.Mar_31_2008

[ccp4bb] xds undefined data_range error

Hello all, Apologies for the non-CCP4 question. I am trying to process some data collected at X6A in March. I edited the XDS.inp file for ADSC detector. When I try to run xds, however, it gives an error immediately: !!! ERROR !!! UNDEFINED DATA_RANGE= I checked the data range and the image path

Re: [ccp4bb] high number of lysines

Hi, Amit If you mostly got clear drops, you might first increase your protein's concentration before you try anything else. Of course, I assume you have a lot of protein, since you are think about doing lysine methylation. Best, Nian On Wed, Jun 10, 2009 at 6:24 AM, amit sharma<3112a...@gmail.com

[ccp4bb] refmac autoweight

Dear All, I am experimenting with manual vs auto-weights in refmac, meditating about the (cor)relation between -(free)LL, wa, and the B-factor restraint weights. Questions arising: 1) is there an authoritative description somewhere on the site what refmac precisely does in auto-weight mode?

Re: [ccp4bb] Transfer crystal from one well (higher precipitant) to another well (lower precipintant)

Hello HengChiat, Could be that the brief exposure to air resulted in more nucleation sites. You could still measure data on your crystal of interest despite the presence of the tiny crystals, as they are not likely to diffract well enough to interfere with the primary diffraction pattern.

[ccp4bb] Transfer crystal from one well (higher precipitant) to another well (lower precipintant)

Hi, My crystal was grown in 33%MPD/0.2M (NH4)2SO4/5% P400/0.1M tris in 500 ul well covered with 200ul paraffin oil. The droplet (0.9 ul protein + 0.9 ul reservoir + 0.2 ul 30% DMSO) is hung over the cover slide. Because of twining issue, when the small but single crystal showed up from the

[ccp4bb] how to use modified dictionary in refmac

Hi I am refining a protein-rna complex structure. The rna has a phosphate group at 5-terminus. I noticed there is a 5p*END in the dictionary list of refmac, so when I loaded a cif file containing lines bleow, # data_comp_list loop_ _entity_mod_id _entity_mod_entity_id _entity_mod_mon_id _entit

[ccp4bb] high number of lysines

Dear All, I have a trimeric molecule (~39 kDa, pI=9.1) carrying 15 lysines in each monomer. I have tried several crystallization screens, however, I mostly get clear drops. The only conditions that I tend to get precipitates in, are the ones carrying citrate. I am beginning to methylate the lys