Re: [ccp4bb] Another paper structure retracted

As the macromolecular crystallography becomes more automated and user-friendly many biologists learn to solve structures and they can make mistakes. Besides, new data become available that can give new ideas etc. I don't think that's so horrible to make an honest mistake and retract papers.

Re: [PyMOL] how to load two separate pdb files simultaneously

Also you can use load A.pdb B.pdb C.pdb or load *pdb leila karami wrote: Dear all very thanks for your time and attention. my problem was solved by load A.pdb load B.pdb

Re: [PyMOL] how to load two separate pdb files simultaneously

I made a mistake. I meant command-line pymol *pdb or pymol A.pdb B.pdb etc. Not load *pdb. Maia Cherney wrote: Also you can use load A.pdb B.pdb C.pdb or load *pdb leila karami wrote: Dear all very thanks for your time and attention. my problem was solved by load A.pdb load

Re: [ccp4bb] Kd's in Crystals

Hi, We had a paper where we looked at Kd of arginine in the arginine repressor-DNA complex (p. 248-249). JMB,2010, *399*, pp.240-254. Maia Jacob Keller wrote: Yes, I think you are right--the somewhat counterintuitive case I was thinking of was, for example, when: Kd = 20nM [L] = 20uM [Po

Re: [PyMOL] [Fwd: Re: select residues from different chains]

Thanks, Zhijian It worked zjxu wrote: Dear Maia, Would you like to try this: select bridge, (c. a and i. 160+356+505+507+508) or (c. c and i. 275+355+128) Best Regards, Zhijian Xu Maia Cherney wrote: Hi Jason, I keep sending my e-mail from a wrong address that the pymol mailing

[PyMOL] [Fwd: Re: select residues from different chains]

Hi Jason, I keep sending my e-mail from a wrong address that the pymol mailing list does nor recognize. I need a command that would allow me to select several residues from two chains, something like that: select bridge, /prot//A/160+356+505+507+508/+prot/C//275+355+128/ But I cannot find

Re: [ccp4bb] crystal bent once open cover slip

You probably use hanging drops. It's the surface tension effect. Check if sitting drops are better. Maia Sitting drops weikai wrote: Hi Folks, We have some membrane protein crystals that are grown in 30%PEG400, 0.1M Na Citrate pH 4.5, 0.1M LiCl. The protein is purified in DDM. The

Re: [ccp4bb] what to do with disordered side chains

I guess, most hydrophilic side chains on the surface are flexible, they don't keep the same conformation. If you cut those side chains off, the surface will be looking pretty hydrophobic and misleading (and very horrible). I prefer to see them intact. I know, most of them are flexible and

Re: [ccp4bb] Detergent/lipid crystal diffraction pattern?

process for you. Maia On 21/03/2011 4:33 PM, Maia Cherney wrote: Hi PS What is the unit cell dimensions in the first crystal? It looks like protein to me. Maia On 21/03/2011 2:03 PM, Pius Padayatti wrote: Hi all, We recently observed some diffraction from membrane protein crystallization

Re: [ccp4bb] Detergent/lipid crystal diffraction pattern?

Hi PS What is the unit cell dimensions in the first crystal? It looks like protein to me. Maia On 21/03/2011 2:03 PM, Pius Padayatti wrote: Hi all, We recently observed some diffraction from membrane protein crystallization drops diffraction that look like non-proteinaceous (please see

Re: [PyMOL] hbs

Hi, Can anybody advise me what is the right command for selecting or coloring many hbs? Instead of color black, hb1 color black, hb2 etc I want something like color black, hb1+hb2+hb3 etc. Maia -- Colocation vs.

Re: [PyMOL] delete an hb from a multiple hb object

Hi Jason, I generated hbs from mode=2 method. It made some wrong hbs. How can I delete those wrong hbs? Maia -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your

Re: [ccp4bb] [Fwd: Re: [ccp4bb] I/sigmaI of 3.0 rule]

Subject: [Fwd: Re: [ccp4bb] I/sigmaI of 3.0 rule] Date: Thu, 3 Mar 2011 10:45:03 -0700 From: Maia Cherney ch...@ualberta.ca Original Message Subject: Re: [ccp4bb] I/sigmaI of 3.0 rule Date: Thu, 03 Mar 2011 10:43:23 -0700 From: Maia Cherney ch...@ualberta.ca

Re: [ccp4bb] weird crystals, I/sigma of 3.0 rule

Hi James, I remember that P1 did not help. That was like 2 years ago. That crystal was very important at that time, so I had to use it. There were many other crystals since then (native, mutants and complexes) in the same space group without problems. But also I had even a more weird crystal

Re: [ccp4bb] I/sigmaI of 3.0 rule

Dear Bernhard I am wondering where I should cut my data off. Here is the statistics from XDS processing. Maia SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONS COMPLET R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno

Re: [ccp4bb] I/sigmaI of 3.0 rule

I have to resend my statistics. Maia Cherney wrote: Dear Bernhard I am wondering where I should cut my data off. Here is the statistics from XDS processing. Maia On 11-03-03 04:29 AM, Roberto Battistutta wrote: Dear all, I got a reviewer comment that indicate the need to refine

[ccp4bb] [Fwd: Re: [ccp4bb] I/sigmaI of 3.0 rule]

Original Message Subject:Re: [ccp4bb] I/sigmaI of 3.0 rule Date: Thu, 03 Mar 2011 10:43:23 -0700 From: Maia Cherney ch...@ualberta.ca To: Oganesyan, Vaheh oganesy...@medimmune.com References: 2ba9ce2f-c299-4ca9-a36a-99065d1b3...@unipd.it 4d6faed8.7040

Re: [ccp4bb] I/sigmaI of 3.0 rule

sense to select a higher cutoff (like what exactly?) and reprocess the data. Maybe one of our data collection specialist should comment on that. BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Maia Cherney Sent: Thursday, March 03, 2011 9:13 AM

Re: [PyMOL] Selecting ASP and GLU

For me, color red, resn asp+glu works. Maia Martin Hediger wrote: Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh# remove water h_add # add hydrogens as

[ccp4bb] [Fwd: Re: [ccp4bb] Space group and R/Rfree value]

Original Message Subject:Re: [ccp4bb] Space group and R/Rfree value Date: Wed, 01 Dec 2010 09:44:06 -0700 From: Maia Cherney ch...@ualberta.ca To: Xiaopeng Hu huxp...@mail.sysu.edu.cn References: 643947201.129232.1291191478190.javamail.r...@zmbx0.sysu.edu.cn

Re: [ccp4bb] diverging Rcryst and Rfree

I found a practical solution to a similar problem. When I get large gap between Rf/R in refmac I repeat the refinement in PHENIX using the same model and the same mtz file, It has always worked for me. And I have no theory for that observation, but the tables in publications looked better.

Re: [ccp4bb] diverging Rcryst and Rfree

I had a similar problem. It dissappeared when I switched the refinement to phenix. The R factors dropped and the difference between them became acceptable.

Re: [PyMOL] map lipophilic potential

Program Vasco can do it. Sebastian Kruggel wrote: dear all, i am looking for a possibility to map lipophilic potential on pymol generated surfaces. i didn't find anything in the documentation and in the mailing list the question came up once

Re: [ccp4bb] Molecular replacement question

Try balbes from G. Murshudov's website. It will find proper search model and use proper truncations automatically. In addition, it will put in your sequence. Paul Holland wrote: Hello fellow crystallographers, I am trying molecular replacement for a protein crystal dataset that has very

Re: [ccp4bb] monomer-dimer

Thank you. Now I understand the difference. I thought there was separation. Maia Xuewu Zhang wrote: Hi Maia, I have seen your post regarding this before and I just want to point out that you may have confused AUC (analytical ultracentrifugation) with gradient-based ultra-centrifugation

Re: [ccp4bb] monomer-dimer

Hi ccp4bb Could you please send me some references with the sedimentation equilibrium calculations of Kd, monomer/dimer ratio etc. Maia Maia Cherney wrote: Thank you. Now I understand the difference. I thought there was separation. Maia Xuewu Zhang wrote: Hi Maia, I have seen your post

Re: [ccp4bb] monomer-dimer

To determine the oligomeric state of a protein (monomer or dimer in your case), it's useful to use the PISA server. You upload your pdb file from the crystal structure.The server calculates the areas of interfaces (buried area) and deltaG (change in Gibbs energy) upon oligomer dissociation.

Re: [PyMOL] pymol dies when minimizing

and PyMOL are you using? Cheers, -- Jason On Wed, Jun 2, 2010 at 10:52 AM, Maia Cherney ch...@ualberta.ca wrote: I had once a problem with pymol that itr would not open from a terminal window. After a long battle with it, the problem was solved after I upgraded my OS. Robin Emig wrote

Re: [PyMOL] pymol dies when minimizing

I had once a problem with pymol that itr would not open from a terminal window. After a long battle with it, the problem was solved after I upgraded my OS. Robin Emig wrote: Does anyone else have the problem where pymol dies, or wont update the display after minimizing on windows? Is there

Re: [PyMOL] coordination bonds

I would like to show coordination bonds between Mg ion and its ligands (oxygens) as broken lines, the distance of Mg-O bond is between 1.9-2.2 A. Maia -- ___ PyMOL-users

[ccp4bb] [Fwd: Is it possible for the Tris buffer to strip the Zn ions from the Zinc Finger motif of a protein?]

Original Message Subject: Is it possible for the Tris buffer to strip the Zn ions from the Zinc Finger motif of a protein? Date: Sun, 23 May 2010 08:45:55 -0600 From: Maia Cherney ch...@ualberta.ca To: ruheng rh_ibp2...@hotmail.com The complex can dissociate

Re: [ccp4bb] Finding best model for molecular replacement

Try balbes. It needs only your sequence and your mtz file. http://www.ysbl.york.ac.uk/~fei/balbes/ Maia Paul Lindblom wrote: Hi everybody, I just crystallized a new project protein. How can I find a possible model for using molecular replacement? I have the sequence of my protein. Is it

[PyMOL] [Fwd: Re: Symmetry Mates Problem]

Docking is very non-reliable. E. Krissinel (2009). /Crystal contacts as nature's docking solutions/. J. Comp. Chem., in press; published on-line 6 May 2009; DOI 10.1002/jcc.21303 Maia humayun scherrif wrote: Hello, Thank you for detailed explanation, surely it is helping me to sort out

Re: [ccp4bb] Is it possible to mutate a reversible epimerase into an inreversible one?

You absolutely right, I thought about it. Maia Marius Schmidt wrote: Interestingly, Maxwell's demon pops up here, wh... , don't do it. If you change the reaction rate in one direction 1000 times slower than in the other direction, then the reaction becomes practically

Re: [ccp4bb] Native Gel Theory and Practice

/ On May 19, 2010, at 1:31, Maia Cherney ch...@ualberta.ca wrote: Dear Jacob, I offer you my opinion. Are you talking about electrophoresis? As far as I know it does not work for the mass. The velocity of a protein depends on the charge at a particular pH, the mass and shape of molecules etc

Re: [ccp4bb] Is it possible to mutate a reversible epimerase into an inreversible one?

I think that it's possible to do a mutation that affects only one way of the reaction. You can mutate a residue that makes contacts only with the product of the direct way or only of the reverse way. Maia Randy Read wrote: Dear Vinson, I would agree with you on choice B. There are probably

Re: [ccp4bb] Is it possible to mutate a reversible epimerase into an inreversible one?

If you change the reaction rate in one direction 1000 times slower than in the other direction, then the reaction becomes practically irreversible. And the system might not be at equilibrium. Maia R. M. Garavito wrote: Vinson, As Dale and Randy pointed out, you cannot change the ΔG of a

Re: [ccp4bb] Is it possible to mutate a reversible epimerase into an inreversible one?

the transition state less stable when approached from the left without making it less stable when approached from the right. Dale Tronrud On 05/18/10 12:34, Maia Cherney wrote: If you change the reaction rate in one direction 1000 times slower than in the other direction, then the reaction becomes

Re: [ccp4bb] Native Gel Theory and Practice

Dear Jacob, I offer you my opinion. Are you talking about electrophoresis? As far as I know it does not work for the mass. The velocity of a protein depends on the charge at a particular pH, the mass and shape of molecules etc. It's very difficult to take all these things into consideration.

Re: [ccp4bb] Unexplained density

I think cacodilate is less likely because it's negatively charged as the carboxy groups that surround the density. I think it's Zn or it may be another (endogenous) metal ion like Ca. You need to look at the coordination. Maia David Schuller wrote: The figures would be more helpful if you

Re: [ccp4bb] program align does not see libcxa.so.5

Hi bb, when I try to run al3 (align) I get the error message error while loading shared libraries: libcxa.so.5: cannot open shared object file: No such file or directory In fact, this file exists. How can I tell al3 where to look for this file? Maia Ed Pozharski wrote: On Fri, 2010-04-30

Re: [ccp4bb] program align does not see libcxa.so.5

'. This doesn't alter the functionality of the program and makes it independent of the intel libraries which most people (notably non-developers) probably don't have on their system. Cheers, Tim On Fri, Apr 30, 2010 at 12:53:49PM -0600, Maia Cherney wrote: Hi bb, when I try to run al3 (align) I get

Re: [ccp4bb] where to find the shell's startup script

most people (notably non-developers) probably don't have on their system. Cheers, Tim On Fri, Apr 30, 2010 at 12:53:49PM -0600, Maia Cherney wrote: Hi bb, when I try to run al3 (align) I get the error message error while loading shared libraries: libcxa.so.5: cannot open shared object file

Re: [ccp4bb] Unexplained density

It's hard to see clearly the density, but judging from the abundance of carboxy groups, it may be a metal. Maia Daniel Bonsor wrote: Hello again I currently have some unexplained density in my structure. As you can hopefully see from the images (see file), the density is dumbbell shaped.

Re: [PyMOL] PyMOL Plugin Architecture

Thank, Robert, Jason. Finally I figured this out with your help. Maia Robert Campbell wrote: Hi Maia, Just to add to what Jason said: On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees jason.vertr...@schrodinger.com wrote: 2. Which plugin allows me to move one structure relative to

Re: [PyMOL] pymol and freemol

/pymol/__init__.py:sys.path.append(freemol_libpy) Hopefully this all helps. -David - Original Message From: Maia Cherney ch...@ualberta.ca To: Jason Vertrees jason.vertr...@schrodinger.com Cc: pymol-users@lists.sourceforge.net Sent: Wed, January 20, 2010 9:37

Re: [ccp4bb] programs to check the structure of DNA

I know two programs; 3DNA by Lu and curves by Lavery and Sklenar. 3DNA is easier to use, it can also make input for the Curves. Maia Alessandra Pesce wrote: Dear All, I am looking for available programs and/or websites able to check the structure of DNA in DNA-protein complexes. I need to

Re: [ccp4bb] protein degradation during concentration for crystallization trials

Hi, MBP tag: 1.there might be a TEV cleavage site in your MBP variant. 2. your protein needs salt to stay in solution 3. your protein forms aggregates with MBP GST tag: you probably concentrate a protease together with your protein. You need a protease inhibitor kit to take care of different

Re: [COOT] pointer distances, recording water

for the wrong subject (pointer distances), as this was my previous request to make pointer distances available to atoms of symmetry molecules. Maia Maia Cherney wrote: Thank you, Paul. There is also difference in recording water. Should it be ATOM or HETATM? Phenix makes it HETATM, but coot makes

Re: [ccp4bb] ccp4 vs. phenix special position atoms

Hi Pavel, you should add to the explanation what /==1 and !=1 are, as the majority of people don't know. / == : equal != : not equal Maia / / Pavel Afonine wrote: Hi Regina, this subject was discussed on PHENIX bulletin board some time ago:

Re: [ccp4bb] Soaking at pH 4.0 ?

Could you transfer your crystals in a higher pH buffer? Maia Paul Lindblom wrote: Hi, I am trying to soak some sugars in my crystals, but the cystallization condition has a pH of 4.0. Does anybody has any experience with acidic oxidation in such a case. I think I can´t avoid oxidation at

Re: [ccp4bb] units of f0, f', f''

(and the density of that). Hans Maia Cherney schreef: Hi all, Usually density means mass divided by volume. The mass of an electron is known. Then it will be no arguments. Maia

Re: [ccp4bb] units of f0, f', f''

Hi all, Usually density means mass divided by volume. The mass of an electron is known. Then it will be no arguments. Maia Ian Tickle wrote: I'm not aware that anyone has suggested the notation rho e/Å^3. I think you misunderstood my point, I certainly didn't mean to imply that

Re: [COOT] moving atoms

Hi Paul, I can not move an atom or a group of atoms in the ligand (rotate/translate zone). The ctrl-click does not work (never works for me on several computers including Mac, PC etc). To move an atom or several specific atoms should not be so difficult. It looks like coot choses how many

Re: [PyMOL] new ideas

, Maia Cherney ch...@ualberta.ca wrote: Hi Jason I need such features. I open two different pdbs and I want to manually move one structure relative to another. I want to dock one structure into another or superpose 2 structures manually. Is it possible? Or I want to move a fragment

Re: [COOT] Coot, delete a chain

Compliance with our Code of Conduct and Policies. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:c...@jiscmail.ac.uk] On Behalf Of Maia Cherney Sent: 31 January 2010 20:07 To: COOT@JISCMAIL.AC.UK Subject: Re: [COOT] Coot, delete a chain Hi all

Re: [COOT] Coot, delete a chain

Compliance with our Code of Conduct and Policies. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:c...@jiscmail.ac.uk] On Behalf Of Maia Cherney Sent: 31 January 2010 20:07 To: COOT@JISCMAIL.AC.UK Subject: Re: [COOT] Coot, delete a chain Hi all

Re: [COOT] Coot, delete a chain

Hi all, Is there a way to delete the whole chain of a complex? Or all solvent atoms at once? Maia

Re: [PyMOL] new ideas

Hi Jason I need such features. I open two different pdbs and I want to manually move one structure relative to another. I want to dock one structure into another or superpose 2 structures manually. Is it possible? Or I want to move a fragment of the molecule relative to the rest of the

Re: [PyMOL] new ideas

molecule cleanup and editing. Try putting your mouse into Editing Mode and moving atoms around. It's not hard. Check this out: http://pymolwiki.org/index.php/Molecular_Sculpting for some help. Regards, -- Jason On Wed, Jan 20, 2010 at 11:52 AM, Maia Cherney ch...@ualberta.ca wrote

Re: [COOT] Release 0.6

Thank you, guys, for the new release. I suggested some time ago to include Go to atom button in the bar beside Display manager, as this is one of the most used buttons. Paul liked the idea, but I don't see it in the new release. Maia Kevin Cowtan wrote: Looks like 2540:

Re: [COOT] Ramachandran plot

Hi Paul, I just figured out the movements in the plot areas. Please, disregard my question. Maia

Re: [PyMOL] [Solved] Upgraded computer, Pymol usable again. :^)

Hi John, I have a similar problem with my ubuntu 8.10. When I use a command window, I get the error message: Traceback (most recent call last): File /var/lib/python-support/python2.5/pymol//__init__.py, line 167, in module import pymol File

Re: [PyMOL] Alignment Objects

Hi, Is it posible in pymol to select all residues of a certain type automatically, like all arginines or all lysines + arginines in a chain? Maia -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008

[PyMOL] pymol does not open from a terminal

Hi, Could you please help me with a pymol problem. I have ubuntu linux and I have pymol in the /usr/bin (comes with ubuntu installation) and also one in the /programs/linux directory. But I can't open pymol in a terminal (both installations), only from applications/education menu. I get this

Re: [COOT] Novel maps...

Hi all, Is it possible to change residue or atom occupancies in coot? Maia

Re: [COOT] mouse buttons and arrow keys [was Re: problems of version 0.6]

, how to enable the middle mouse drag for translate? (Chording on the mouse is fine with me, too). Thanks for the arrow keys for translate. Maia Paul Emsley wrote: Dear Maia, Maia Cherney wrote: I would like to use only one-button keys, so that I could use only one hand when fitting

Re: [COOT] problems of version 0.6

to program arrow key for translation. Could you give me a script for that, I can't write it myself. Maia Paul Emsley wrote: Maia Cherney wrote: The general torsion function is not as good as the torsion in old X-fit. Are you or have you ever been a member of the von Delft Pressure Group? In x

Re: [COOT] problems of version 0.6

Thank you, Bernhard The buttons I like to change are internally assigned. For example, I would prefer to use key b to move backwards through residues of a chain. Right now you need two hands for that (shift-space). To drag the map, again, you need two hands (ctrl-left mouse). I would like to