Re: [ccp4bb] How to overlap DNA

Dear Guys, Thank you very much for your suggestions! I have tried Superpose from CCP4i as suggested by Arka Nicolas. It works fine and can overlap the whole base as the LSQ in coot. The USF (lsqman suggested by Tim)has not been installed in my PC and I will try it and see after it has been

[ccp4bb] how to overlap DNA

Dear All, Does anybody has the experience to overlap DNA in the protein complex? I have tried the LSQ in Coot and it works ok but not perfectly. Could you please tell me a better way to do that?Or can Coot be used to overlap DNA/RNA on their back bone by LSQ or SSM ? At the same time,

[ccp4bb] How to fit the crystal structure into the em model(not the real data but the vrml file)

Hello, I am working on a protein whose EM model has been built long time ago. The crystal structure has been solved recently and I want to know the difference between the crystal structure and EM model. Unfortunately there is no data in the EM data base, so I can not use Chimera or Phaser to

Re: [ccp4bb] protein crystallization problem

Have you ever tried the condition of AS as precipitant and PEG as the additive? They have opposite functions on your protein's solubility:one increases and decrease it. Maybe you can vary the ratio of them to control your protein's solubility. And the xtals may be seen in some conditions.

Re: [ccp4bb] Warren DeLano

I can not agree you more. I was totally shocked by this bad news and can not believe it at all. I do not know Warren but use Pymol quite a lot. It is very sad to see one friend who is still very young away from you. Could we rename the Pymol to remember Warren? He will be remembered by all

Re: [ccp4bb] Problem about Molecular Replacement with identity 30% model

孙建 wrote: Dear all: Recently,I have a problem about molecular replacement with identity 30% model. There are two moleculars in AU.Through self-rotation analyze,there are a two-fold axis in AU along X axis or Z axis.Then I rotate and translate the model with CNS MR module. several

Re: [ccp4bb] Refmac specific questions

Hi Partha, It should be depended on the input model : MIXEd Some atoms with isotropic, some with anisotropic B-values. In this case input file (PDB) defines which atom should be refined isotropicly and which anisotropicly. The atoms with ANISOU card are refined anisotropicly. ta

Re: [ccp4bb] Building PEG-400 in Coot

Hi Partha, You can either fit them as two PEG400 or manual build a model of PEG-PEG using Sketcher. I do not think it is necessary to do that in the second way. ta leo Partha Chakrabarti wrote: Hi, Could someone point me to the best ways of building a non standard ligand? I had PEG-400 in

Re: [ccp4bb] structure alignment based on the ligand

Coot can do that. You can use lsq to overlap the whole atoms of ligands. Another way is using LigAlign in Pymol. Good luck! leo rui wrote: Hi, All I have dozens of complex structures ( protein + ligand ) and want to align the structures based on the ligand. Does anyone know such kind of

Re: [ccp4bb] How to loop up crystal from AmSO4.

One way to do that is lower the concentration of AS form 0.2 to 0 or as low as you can . This is depended on the xtal's stability . You can transfer them directly or step by step. Otherwise you can try to add water around the drop to increase the humility or cover the drop by oil. Good luck!

Re: [ccp4bb] [ANNOUNCE] Journal of Failed Crystallization Experiments

What is the impact factor for that? 100 or 1000? leo ar...@xtals.org wrote: Hey, This is *the* place to report my experiments with Uranium (IV) Astatide (UAt4) and Radon for phasing! Artem Dear Crystallography Community: ... good stuff ... Sehl Oediter Chief Guy in Charge

Re: [ccp4bb] how to present the electron density map

You can transfer the omit map from cns format to ccp4 or o map using mapman . Then you can load and show it in pymol. Good luck! liu xu zhen wrote: Hi,everyone, I want to present the ommit density map on my structure, It will be great if someone can suggest the software and a brief

Re: [ccp4bb] How to refine a solution obtained by molecular replacement

Hi Sun, For 2.5A data you can try phenix or arp/warp to autobuild the the model using the phase form MR ,then you can get the most of model you want if you are lucky enough or you need more manual bulding or another cycle MR again . Good luck! liu Sun Tang wrote: Dear All, Recently I

Re: [ccp4bb] Refmac library trouble -

Hi Jon, I do not think the lib you got from ligand dep is enough to be used in the refmac. Unfortunately I can not find or make the library from PRODRG2 server because the FE can not be handled by that server right now. So maybe you should make the library yourself : either using sketcher

Re: [ccp4bb] Refmac library trouble -

The right library should be HEO_mon_lib.cif Good luck! leo Jonathan Marvin Caruthers wrote: All: I'm trying to run Refmac with a heme not present in the default libraries. Unfortunately, I can't get the library sketcher to create a library description file and get the following error

[ccp4bb] superpose structures .ssm or lsq which is better

Dear All, I am overlaying several structures using coot. There are two ways SSM or LSQ can be used in that package. But I got clearly different result form the two methods. In my opinion SSM only works on the secondary structures and LSQ can works on the whole atoms ,main chain or CA. So

Re: [ccp4bb] site mutation evaluation

Coot ,Pymol or Mumbo are all software can be used to mutate residues of PDB. Rotamers can adjust by Coot and you can use Mumbo to do energy minimisation .As for Pymol ,the powerful fig maker ,is not good choice to do this . Maybe Chimera is another choice . But I have not use it before. So

Re: [ccp4bb] site mutation evaluation

Hi Hongmin, That should need some docking softwares or the structures of the complex. ta liu Hongmin Zhang wrote: Thanks! I think we still can't tell if the mutant would disturb ligand binding or not. Best! Hongmin On Wed, Dec 3, 2008 at 2:15 PM, Juergen Bosch [EMAIL PROTECTED] mailto:[EMAIL

Re: [ccp4bb] protein crystal decay problem

How about 90? If it is ok , maybe you need more than 3 or more xtals to collect the whole dataset and merge them together. Otherwise your xtals should be the anisotropic .You'd better to collect images in the better region or screen more xtals to get better ones. Good luck! leo lei feng wrote:

Re: [ccp4bb] electrostatic surface with Ca

Hi,Philippe, Have you tried to use Grasp or APBS in Pymol directly to do that? I think they should work on the ions such Ca or others. Good luck! leo Philippe Leone wrote: Hi everybody, I'd like to generate an electrostatic surface containing a Ca ion. I tried to generate a pqr file

Re: [ccp4bb] Truncated protein structure

Hi ,Haitao , If I were you ,the first thing I will do is to check xtal using MS and N-terminal sequencing to know what it is . These need to be done anyway. At the same time ,try to use the ways describe by other people to handle the data and search for solution using truncated model

Re: [ccp4bb] Density is not clear

Hi,John, I faced the similar situation before even the resolution about 2.4. At that region the residues are all hydrophobic ones and should be very flexible . Arp/warp and phenix do not work well and resolve does not improve the density either. At the end I just try to build the model as

Re: [ccp4bb] negative LLG in Phaser run

Dear Oganesyan, That means the second component is not right based on the number of LLG and PACK. Please see that for more details. http://www-structmed.cimr.cam.ac.uk/phaser/faq.html You should check that model and redo MR again. Good luck! leo Oganesyan, Vaheh wrote: Phaser experts,

Re: [ccp4bb] 3D structure based alignment

Hi, You can use Chimera to do the work . Good Luck! liu Tânia Oliveira wrote: Hello, I´m having a problem that I would like to know if someone could help me. I want to do a 3D structure based alignment of my protein with another one. The problem is that my protein has 2 domains, and the

Re: [ccp4bb] expression vector

Hi,Yang, Tag(type and length) ,surface charge and crystallization condition are parameters which affect the packing in the crystal. It should be the tag or mutation not the the vector itself made you get different unit cell. ta liu 杨柳青 wrote: Hello,everyone! I have a question,is the expression

Re: [ccp4bb] Correct the dihedral angles

Li Yang, I usually use three ways to solve that: 1 CNS anneal 2 coot edit backbone torsions and the last redo manual build as Paul's suggestions for low resolution data in COOT FAQ if you using coot and the resolution of your data is low Good Luck! liu yang li wrote: Dear all, Does

Re: [ccp4bb] crystallization robot

Douglas Oryx6 or 8. It works well on sitting drop and microbatch in our division. Nalam, Madhavi wrote: Hi, Sorry for the non-ccp4 related question. We are planning to buy a crystallization robot. We looked at the 'Mosquito'. We felt it is good for setting 96 well plates (for screening the

Re: [ccp4bb] how to model glycosylated residues?

Hi Jiamu, You can use Sketcher to make the library for Coot. You'd better to get the PDB file from http://www.dkfz.de/spec/glycosciences.de/tools/pdbcare/ . Good luck! liu Jiamu Du wrote: Thanks for all the replies above. I have pasted the figure of the electrondensity map in the attachment.

Re: [ccp4bb] How to refine large moleculars?

Have you tried TLS and NCS? Maybe these can lower the R free a little. But ,the quality of your model depends on the quality of your data and completeness of your model etc. Yongchao Li wrote: I have a large molecule to refine.There are about three thousand residues in one asymmetric unit.

[ccp4bb] problem with refmac refinement

Hi, All, I am trying to refine a model with ligand. The problem is: The electron density of ligands can be seen on the map prepared by resolve . After rebuilding the ligand into the model by coot and refienment using refmac, the electron density of the ligands was very poor on the map