Re: [ccp4bb] Protein cavity volume calculation
Hi Seema, you can try the following servers, may be they will be fine for you: https://mole.upol.cz/ http://sts.bioe.uic.edu/castp/index.html?2was http://altair.sci.hokudai.ac.jp/g6/service/pocasa/ Best P.P On Sun, Jun 16, 2019 at 7:38 PM wrote: > Dear Seema, > > Here are the links to two older bb threads discussing this topic: > > http://www.ysbl.york.ac.uk/ccp4bb/2000/msg00702.html > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;c74cbd36.1801 > > HTH, > > D > > > > > > > I was wondering if anyone could recommend a good program or links to > > calculate the cavity volume of the protein active site. > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] PDBcur fails with error message
Dear All, Here is the CCP4 version 6.5 installed, where I want to remove the ANISOU atoms from the pdb file, but its shows failed job with an error message : has failed with error message child process exited abnormally So I am not able to figure it out, how to rectify. Please suggest. Thank you Regards Jeorge
[ccp4bb] error message in xds
Dear All, I am getting an error message after indexing the data in XDS as !!! ERROR !!! DIMENSION OF DIFFERENCE VECTOR SET 2 , please suggest what wrong has happened and what could be done for this, initially the message was insufficient number of spots accepted was there, then I change the resolution range from 20 3.5 to 20 0 0 0, then I got the above mentioned error. Thank you in advance. Jeorge
Re: [ccp4bb] PHASER MR solution
Thank you so much to all for your kind concern. Jeorge On Mon, Jan 26, 2015 at 5:55 PM, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: Dear Jeorge, you'll find some information about this in http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination . A practical and easy way is described in http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless HTH, Kay On Mon, 26 Jan 2015 11:24:27 +0100, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Jeorge, XDS make no claim to determine the SPACE GROUP but rather the LAUE GROUP, as only the latter is taken into account during data integration. This is definitely so during the indexing step (IDXREF.LP), but even in CORRECT, when systematic absences are sometimes indicated, XDS does not really choose the space group. Best, Tim On 01/26/2015 05:46 AM, jeorgemarley thomas wrote: Hello Dr. Randy Here is the IDXREF.LP I got in which, on the basis of quality of fit, I went for this space group well I would also try for the other screw axes. So should I Integrate the data from beginning with all possible screw axes of orthogonal space group? I am attaching the IDXREF.LP screen shot here. Jeorge On Sun, Jan 25, 2015 at 5:00 PM, Roger Rowlett rrowl...@colgate.edu wrote: Did you search all 8 possibilities of screw axes, e.g. P2221, P21212, P212121, etc? Roger Rowlett On Jan 25, 2015 4:50 AM, jeorgemarley thomas kirtswab...@gmail.com wrote: Hi, I have processed the data using XDS and space group found to be P 2 2 2 (16) and I used the phaser MR for first phase determination. The model I have used has has more than 70 % sequence identity, when I run the phaser I got the message which I have attached here. And only sum. file I got as an output. Does any one have suggestion what should I do ? I would highly appreciate your kind suggestions. Thank you in advance. -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] Visualizing Stereo view
Dear all, First of all sorry to put this off topic and silly question on bb. Can anybody suggest me, how to create a stereo image and how it is different from the normal. How can I visualize it, if anybody has answer for this please suggest me its significance in analysis. Thank you very much in advance. Thanks Jeorge
[ccp4bb] Restraints after refinement
Dear all, I am working on my molecule, but after running Refmac5 restrained refinement the bonding distances and angles are broken. I used Phenix to create the ligand and used Coot to place the ligand into the correct location in the molecule, merged the ligand and molecule coordinates, and saved the file. Then I went to run restrained refinement on the merged coordinates using the cif file provided from the phenix to the refmac library,the rest of the settings were set at the defaults. During fitting the model in the 2Fo-Fc map of the ligand there were no issue, but it fitted well and after refinement of the same, the bond breaks and distorted as observed in coot. The resolution is 1.6 Ang. phosphate linkage bond is broken. What could be the best possible reason for this and what can be solution for this ? Could you please suggest what should I do for a complete model for the ligand ? I would like to run a round of restrained refinement without breaking any geometric restraints that should be imposed on my ligand. Thank you for your help in advance, Jeorge
[ccp4bb] Water molecules after refinement
Dear All, I am sorry to ask this simple question, but I really need suggestions for this. As the refinement has been done at 3.0 Angstrom after refinement the water molecules were added by using find waters in coot. After adding water refinement was done using Refmac 05. Now when I look on the added water molecules some has density around it and some does not (even no red density around it). Should I remove later water molecules. and again do the refinement ? Please give some explanation also for this. as the R free and R meas has reduced to some extent, also the r m s d contour of map level was kept at 1.09 after refinement. I welcome your suggestions, thanks in advance. Regards Jeorge
[ccp4bb] Adding water molecule and metal atom
Hi All, First of all sorry to ask such simple question over here. I have added water molecule in my protein molecule in coot, also some Ba atom. I have added the water molecule manually as when it was added automatically the water added everywhere it find lobes of electron density. And also when I add Ba atom it gets converted as water molecule. Your kind help will be greatly appreciated Regards Jeorge
