[ccp4bb] Rename chain ID of water molecules

Dear CCP4BB members, I want to keep the chain ID of water molecules the same as their interacting protein molecule. For example, I have two protein molecules in the structure —— named chain A and chain B; then I want all the water molecules interacting with protein A (or B) have the same chain

Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?

Of course, if you can plan ahead, you can grow your crystals in shipping friendly plates. See the In-Situ plate at Mitegen for details. http://www.mitegen.com/mic_catalog.php?c=insituplates you also might try to add agarose to the drop to fix the crystal in place, but that could be tough with a

[ccp4bb] twin or untwinned

HI all, I have a data set processed to P42 21 2 (the space group was suggested by pointless ). then I use phenix.xtriage to analysis the data. I was confused by the phenix.xtriage result. According to the following number it is twin data, but why it couldn’t find any possible twin law? De

Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?

Hi Meisam, Here is what I have done before: 1. transfer the whole drop to a capillary and close both sides with plasticine. Notice that I am talking about the whole drop, not individual crystals. It is a lot simpler this way and involves less crystal manipulation. Make sure you remove any skin if

Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?

Somebody really needs to hurry up and invent a molecular beam transporter you know like the one on Star Trek. Then we could just send our crystals wherever we want it that way. Sorry rough day in the lab. But if we could do that, we probably wouldn't need to solve structures anymore anyway. I have

Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?

Hi Meisam - We do this frequently, using pieces of spongy foam to pad the inside of a sturdy styrofoam shipping box, which keeps the temperature from fluctuating too much. This is then carried in a reusable grocery bag by one person whose sole responsibility it is to ensure it isn’t subjected

Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?

Another thing I always did when traveling with trays was pack them surrounded by ‘blue Ice’ packets (or the equivalent) equilibrated at the same temperature at which the trays have grown. It prevents the trays from moving around in the transport box (I used a small plastic Coleman cooler with

Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?

Dear Meisam I second what Nicolas had suggested: to mount your crystals in glass capillaries. I used to do this when travelling to the ESRF from the UK, keeping the crystals in a plastic case (alternatively, you may prefer using the Granada Box from Hampton Res. for this). One important considerat

Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?

You can prevent them from falling off by also removing 5 microliter or so of mother liquor from the drop and repositioning it back over the reservoir On Wed, Jul 2, 2014 at 3:38 PM, Patrick Loll wrote: > You can cut a small piece of sponge and put that into the reservoir; this > prevents the re

Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?

Dear Meisam, i don't know exactly what you need to do after the transfert, but if you want collect without frozen, maybe you can try to use capillar. Maybe can you mount your crystall in capillar before the travel ? It's simple suggestion, i never did that. Nicolas _

Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?

You can cut a small piece of sponge and put that into the reservoir; this prevents the reservoir buffer from splashing up into the drop. The sitting drops should be reasonably safe, but the 10 uL hanging drops are big; they'll be vulnerable to falling off if the tray is jarred. Good luck! Pat

[ccp4bb] How to transfer non-frozen crystals with less disturbance?

Dear CCP4ers I need to transfer some crystals mainly in sitting drops to the site of data collection without freezing them. I do not know what is the best solution to secure the boxes in their place to minimize the disturbance. I am using the 24 well VDX plates with 10-80 microliter sitting d

Re: [ccp4bb] Solvent channels

Hi Reza, I can recommend the work of Marc-Olivier Coppens and Kourosh Malek and the references therein for an interesting journey through solvent channels. David Hargreaves Associate Principal Scientist _ AstraZeneca Discovery S

Re: [ccp4bb] Buried surface area calculation..

Dear Gajana, you can use . PISA ((Krissinel and Henrick, 2007) (EMBL server) and NACCESS (Hubbard and Thornton, 1993). (not for windows i think). Hope to help Nicolas De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Gajanan Arbade [gajana

Re: [ccp4bb] Solvent channels

Sorry for the delayed response - The situation of 'normal' drug-lead molecule, no restriction of solvent channel access, no other hindrance to mobility, and rapid on-rates and/or/with a low Kd driving/maintaining the concentration gradient might be considered almost optimal. But let us assume th