Re: [ccp4bb] Optimum figure of merit

modification > in > order to get to an interpretable (extensible) density map. > > Best regards, > Tim > > > On Monday, November 07, 2016 02:31:39 PM Kavyashree Manjunath wrote: >> Dear users, >> >> What is the acceptable values for the figure of merit (FOM) >> for

[ccp4bb] Optimum figure of merit

Dear users, What is the acceptable values for the figure of merit (FOM) for an MR solution (where the model is atleast 99% identical). what is it in case of solution from direct methods? Thank you Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner,

[ccp4bb] IUCR bibtex

Dear users, Sorry for an off topic question. I would like to request if anyone can mail me the iucr.bst file for bibtex. The website hosting this file is not opening. Thank you Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to

Re: [ccp4bb] IUCR bibtex

Dear Sir, Yes. This link is not opening. Thanks for sending the file. Regards Kavya Hi Kavya, If you mean the file located at ftp://ftp.iucr.org/templates/latex/iucr.bst I have just sent it to you. Best regards, Folmer 2014-08-18 7:23 GMT+02:00 Kavyashree Manjunath ka

[ccp4bb] Number unique reflections (all)

Dear Users, Which value in scala log file indicate the Number of unique reflection (all) that needs to be entered during the deposition of structure in RCSB. Thank you Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be

Re: [ccp4bb] Calcium ions in enzymes

Hi, Also Secreated Phospholipase A2 enzyme requires Calcium for its catalysis. Regards Kavya On 5/31/13, Patrick Loll pat.l...@drexel.edu wrote: staph nuclease On 31 May 2013, at 6:25 AM, Wei Liu wrote: Dear all, As we all know, many proteins contain calcium ions. Does anyone know if

Re: [ccp4bb] AW: [ccp4bb] Short contact between symmetry equivalents

this and with occupancies around 0.5 your validation problem would be solved and your model would probably be closer to the true situation in the crystal. My 2 cts, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Kavyashree

[ccp4bb] Short contact between symmetry equivalents

Dear users, Is short contact (1.83Ang) between an atom and symmetry equivalent of itself tolerated during deposition? I am not able to get rid of this short contact appearing after refinement. Thank you Regards Kavya -- This message has been scanned for viruses and dangerous content by

Re: [ccp4bb] Short contact between symmetry equivalents

of nature. It's fairly common to have, say, a water molecule split in two positions near symmetry axis - as long as you have it at occupancy1.0, it's ok. On 05/27/2013 05:21 AM, Kavyashree Manjunath wrote: Dear users, Is short contact (1.83Ang) between an atom and symmetry equivalent

Re: [ccp4bb] Short contact between symmetry equivalents

Sir, Ok yes. I tried with 0.5 occupancy, ended up getting positive density around acetate on both sides equally. Later I tried with 0.8, 0.99 for which the map was normal and also validation did not report it as short contact. Is it ok if I give 0.99 occupancy? Thank you Regards Kavya It does

Re: [ccp4bb] Negative FoFc around ligand

! Best, Tim On 05/25/2013 06:55 AM, Kavyashree Manjunath wrote: Dear users, I tried giving occupancy of 0.65 and 0.6 respectively for all atoms of the two ligands and refined. Now after refinement, the atoms of ligand does not have negative density but those which did not have negative density

Re: [ccp4bb] Negative FoFc around ligand

:40, Kavyashree Manjunath ka...@ssl.serc.iisc.in wrote: Dear Sir, Thank you all for your kind advice and clarifications. I will keep the occupancy 1.0 for both the ligands and refine without considering the negative density in this case. Thanking you Regards Kavya -BEGIN PGP

Re: [ccp4bb] Negative FoFc around ligand

by a conformationally unrestricted bond? These quite often have poor density. Hard to judge without seeing the actual density - but understand why! Regards, Antony. Sent from my iPhone On 25 May 2013, at 10:40, Kavyashree Manjunath ka...@ssl.serc.iisc.in wrote: Dear Sir, Thank you all

[ccp4bb] Negative FoFc around ligand

Dear users, I am using refmac 5.7.0029 for refining a structure (resolution 2.2 Ang) bound to 2 ligands. After MR There is a very clear density of ligands but after refinement, I get negative fofc map near one of the ligand upto 5 sigma. However its 2fofc map covers the whole ligand. Also for the

Re: [ccp4bb] Negative FoFc around ligand

the 'occupancy' keyword in refmac to refine it. The density maps should improve. Best, Tim On 05/24/2013 06:50 PM, Kavyashree Manjunath wrote: Dear users, I am using refmac 5.7.0029 for refining a structure (resolution 2.2 Ang) bound to 2 ligands. After MR There is a very clear density

Re: [ccp4bb] Negative FoFc around ligand

most likely has reduced occupancy. You can either manually set all atoms in the ligand to e.g. 0.5 or use the 'occupancy' keyword in refmac to refine it. The density maps should improve. Best, Tim On 05/24/2013 06:50 PM, Kavyashree Manjunath wrote: Dear users, I am using refmac 5.7.0029

Re: [ccp4bb] Negative FoFc around ligand

)? Is it possible that your ligand binds in different orientations? So your atom X could actually be atom Y? Debasish -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kavyashree Manjunath Sent: Friday, May 24, 2013 1:12 PM To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Negative FoFc around ligand

- assuming you have already done a thorough refinement. Zhijie -- From: Kavyashree Manjunath ka...@ssl.serc.iisc.in Sent: Friday, May 24, 2013 12:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Negative FoFc around ligand Dear users, I am using

Re: [ccp4bb] Negative FoFc around ligand

-- From: Kavyashree Manjunath ka...@ssl.serc.iisc.in Sent: Friday, May 24, 2013 12:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Negative FoFc around ligand Dear users, I am using refmac 5.7.0029 for refining a structure (resolution 2.2 Ang) bound to 2 ligands. After MR There is a very

[ccp4bb] A small clarification

Dear users, I wanted a small clarification, I was solving a ligand data in H3 space group with a dimer as the asymmetric unit. Initially, I had solved and refined this without using the same Rfree reflections as that of native data. So I resolved and refined the same data by considering the

Re: [ccp4bb] A small clarification

and the data processing program may have chosen different ones in your case. (not sure if this is the case for H3, I know it is for P321 because I have experienced it...) On 3 May 2013, at 10:07, Kavyashree Manjunath wrote: Dear users, I wanted a small clarification, I was solving a ligand data

Re: [ccp4bb] A small clarification

!! Thank you Regards Kavya -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kavyashree Manjunath Sent: Friday, May 03, 2013 10:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] A small clarification Dear users, I wanted a small clarification, I

Re: [ccp4bb] A small clarification

be a crystallographically acceptable fit Eleanor On 3 May 2013 10:02, Kavyashree Manjunath ka...@ssl.serc.iisc.in wrote: Dear Sir, There used to be a chaos with H3 and R3 settings so you first thing you might want to check that the same setting is used in both cases. Easiest would be to check the CRYST1

[ccp4bb] Refinement using SAD

Dear users, I have a ligand bound data with anomalous signal (due to Cd at wavelength 1.5417Ang). The structure was solved using the native structure as MR model. Both native and ligand data were crystallised in same space group. 1. Native was refined using no prior information option in refmac.

Re: [ccp4bb] Anomalous atom or ligand?

.. If possible I like to use these as bench marks for P. But in my experience the P are often even weaker - maybe the ligand is not fully occupied, or the P temp. factors are higher? On 24 April 2013 10:56, Kavyashree Manjunath ka...@ssl.serc.iisc.in wrote: Dear users, After detecting

[ccp4bb] Anomalous atom or ligand?

Dear users, After detecting the anomalous peaks in a data, Is it necessary that there will be an anomalous atom in most of the peaks? In a particular case, a low ranking peak was assigned an anomalous atom because it was present in the native structure, while a peak with a rank higher than this

[ccp4bb] Too high function value for reflection ... refmac

Dear users, While refining the structure, I get a message in the log file - Too high function value for reflection 408 0 103.7139 Too high function value for reflection2766 0 110.8577 Too high function value for reflection3439 0

[ccp4bb] Refinement with anomalous signal

Dear users, The native structure for a protein is available and there is a ligand bound data. The crystallisation condition has anomalous scattering metal ions (Cd). Both the data are scaled by separating anomalous pairs. So while refining a ligand bound data with a solution obtained using

Re: [ccp4bb] Refinement with anomalous signal

refinement the R factors can be significantly improved as well. I would give it a try. As far as the other options in refmac such as inclusion of H-L coefficients or phase, FOM, I believe that direct refinement against the SAD data is preferred. Philip On Fri, Apr 19, 2013 at 7:43 AM, Kavyashree

Re: [ccp4bb] Refinement with anomalous signal

peaks really are two different fully occupied atoms with a lesser anomalous signal than expected. Best, Tim On 04/19/2013 02:02 PM, Kavyashree Manjunath wrote: Sir, Thank you Sir. I tried this once at the end in order to check the refinement statistics, R, Rfree and FOM showed improvement

Re: [ccp4bb] Angle restraints

to worry less. Cheers, Robbie Sent from my Windows Phone From: Kavyashree Manjunath Sent: 2013-04-15 07:13 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Angle restraints Dear users, Validation of a structure showed a deviation in the angle between atoms

Re: [ccp4bb] Angle restraints

Sir, Thank you Sir. It worked. I used alternate conformations which differ by 180 deg around CZ-NE bond. Now there is no angle deviation error. Thank you all for useful suggestions. With Regards Kavya what you may have is two alternate conformations - i.e. your current one and one with the

[ccp4bb] Angle restraints

Dear users, Validation of a structure showed a deviation in the angle between atoms NH1-CZ-NE and NH2-CZ-NE in the arginine residue. Several trials of modification of the orientation failed to solve this problem. I also confirmed by deleting the side chain and refining, it confirmed the presence

[ccp4bb] Ligand occupancy refinement ~2.0Ang

Dear users, Is it advisable to refine the occupancy of a ligand for a 2.0Ang data by approximately changing the values of occupancy based on its b-factor? After refinement, there were some negative densities appearing in some parts of the ligand, like at the centre of a pyrimidine ring, so I

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

. R On 12 Apr 2013, at 17:12, Kavyashree Manjunath ka...@ssl.serc.iisc.in wrote: Dear users, Is it advisable to refine the occupancy of a ligand for a 2.0Ang data by approximately changing the values of occupancy based on its b-factor? After refinement, there were some negative

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

Thank you Sir. With Regards Kavya So there is a CCP4 GUI Just prepare a txt file with the relevant occupancykeywords and use it in the GUI under 'Refmac keyword file' Best R From my iPhone On 12 Apr 2013, at 19:50, Kavyashree Manjunath ka...@ssl.serc.iisc.in wrote: Respected

Re: [ccp4bb] Rfree flag

Dear All, Thank you Folmer and Fred for your suggestions. Mine is an isomorphous crystal. I had refined without using the same set of Rfree reflections, finally getting larger difference between the R and Rfree. I hope considering the same Rfree set would solve this problem. Thank you With

[ccp4bb] Rfree flag

Dear users, Is it mandatory to use the same reflections for Rfree calculations of a ligand bound data as that of its native? Thank you With Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

[ccp4bb]

Dear CCP4 users, It is extremely sad that CCP4BB has failed to moderate/screen for such spam mails! Thanks kavya Dear Friends, There is no need to apply to this position, we suggest. It is a PREDETERMINED SELECTION, i.e. candidate is fixed and this (advertisement, screening,

[ccp4bb] Anion-Pi interaction in protein

Dear users, Has there been any instances where there is an anion-pi interaction in proteina. I found a density that could accommodate an acetate ion just above the aromatic ring of the tyrosine residue in the protein I am working on. I just came across an article regarding the anion-pi