[ccp4bb] About SAD phasing
Hi, All I would like to ask whether is it possible to allocate the Se site and obtain the phase by just using the SAD data set (no native dataset used)? Thanks, Qing
[ccp4bb] domain contact surface
Dear all, I am trying to calculate the domain-domain contact surface from one chain. I see AREAIMOL to only tell you the accessible surface area/residue. Could any other software/webserve could specify residues in the contact surface and calculate the total contact area? Thanks J.
Re: [ccp4bb] domain contact surface
Ed Pozharski wrote: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Try PISA server - it will identify contacts and report total buried surface area per contact. On Fri, 2010-02-19 at 16:42 +0100, Jane Bailey wrote: Dear all, I am trying to calculate the domain-domain contact surface from one chain. I see AREAIMOL to only tell you the accessible surface area/residue. Could any other software/webserve could specify residues in the contact surface and calculate the total contact area? Thanks J. Dear all, Thanks very much for the answers. I managed to get the interface from PISA by assign two chain IDs onto two domains, as suggested by Pierre and Amy. It gave the interface Solvent-accessible area of each domain: 274.2, 312.2, but not the BSA. However I saw it gave the BSA of individual residue from the interface. Do people get the total interface BSA by adding them up? best Jane
[ccp4bb] To calculate Domain-domain orientation
Dear all, Problem is coming one after another. I got another question about how to calculate the domain/domain orientations (tilt and twist angles). Sorry I probably disturb a bit often I searched a lot, but no publication says how it was calculated. Does anybody know anything about this? Thanks a lot! Jane
[ccp4bb] DSSP server
Hello all, I am sorry for this off-topic question. I see it has been discussed many times, but somehow I got stuck in the very beginning. I want to assign ss to my pdb file in DSSP, but I could not find a server to run it. Does anybody know a webserver where I could run this kind of tasks? I use iMAC. Many thanks! Jane
[ccp4bb] xds process gave different cell parameters
Hi I was processing my data with XDS several runs, they gave slightly different cell parameters everytime, eg: 1) 77.100 103.850 116.550 90.00 90.00 90.00 P 21 21 21 2) 77.086 103.821 116.533 90.00 90.00 90.00 P 21 21 21 I have already a refined model from 1), can I use this model to refine against dataset 2) by simply change the cell parameter in the pdb file? There's nothing wrong with dataset 1), just wonder whether it is doable . Many thanks Jane
[ccp4bb] refmac problem
Hello again I am refine my model using TLS and restrained refinement, and I got below the error message from refmac although the program claim to be successful. There is no output mtz and pdb files. Any suggestions are appreciated! Many thanks! Jane ***TLS refinement cycle***7 1 0.26529309 0.40231493 0.31580201 -5.07818013E-02 0.17374255 -0.39783996 2.04001069E-02 7.82079645E-04 1.11576570E-04 -3.76230048E-04 -2.82397377E-04 -1.06552179E-04 4.59514521E-02 -2.79289447E-02 -1.72524340E-02 -1.04173245E-02 -1.80899426E-02 -7.60819018E-03 8.42294842E-03 1.78668604E-04 -2.46240292E-02 Problem xyz 6193 -16.111391 -2.8551121 -5.0709343 -4.46808338E-03 0.43998715 0.84659839 0.22162700 -0.42724574 0.15069498 -0.42246437 -4.46808338E-03 0.21654272 1.2961377 0.22026606 0.85707664 -0.46572798 imac4:~ jbailey$ ccp4i Top level CCP4 directory is /sw/share/xtal/ccp4-6.1.2 Using CCP4 programs from /sw/share/xtal/ccp4-6.1.2/bin 15:03:39 MoveFile: input file /tmp/jbailey/native_580_24_2_pdb_1.tmp does not exis t 15:03:39 MoveFile: input file /tmp/jbailey/native_580_24_3_mtz_1.tmp does not exis t 15:03:39 MoveFile: input file /tmp/jbailey/native_580_24_4_tls_1.tmp does not exis t
[ccp4bb] refmac problem
Hello again I am refine my model using TLS and restrained refinement, and I got below the error message from refmac although the program claim to be successful. There is no output mtz and pdb files. Any suggestions are appreciated! Many thanks! Jane ***TLS refinement cycle***7 1 0.26529309 0.40231493 0.31580201 -5.07818013E-02 0.17374255 -0.39783996 2.04001069E-02 7.82079645E-04 1.11576570E-04 -3.76230048E-04 -2.82397377E-04 -1.06552179E-04 4.59514521E-02 -2.79289447E-02 -1.72524340E-02 -1.04173245E-02 -1.80899426E-02 -7.60819018E-03 8.42294842E-03 1.78668604E-04 -2.46240292E-02 Problem xyz 6193 -16.111391 -2.8551121 -5.0709343 -4.46808338E-03 0.43998715 0.84659839 0.22162700 -0.42724574 0.15069498 -0.42246437 -4.46808338E-03 0.21654272 1.2961377 0.22026606 0.85707664 -0.46572798 imac4:~ jbailey$ ccp4i Top level CCP4 directory is /sw/share/xtal/ccp4-6.1.2 Using CCP4 programs from /sw/share/xtal/ccp4-6.1.2/bin 15:03:39 MoveFile: input file /tmp/jbailey/native_580_24_2_pdb_1.tmp does not exis t 15:03:39 MoveFile: input file /tmp/jbailey/native_580_24_3_mtz_1.tmp does not exis t 15:03:39 MoveFile: input file /tmp/jbailey/native_580_24_4_tls_1.tmp does not exis t
[ccp4bb] to extract protein sequence from a rebuilt pdb file
Hi, all I am currently rebuilting my structure in coot, and the protein sequence is around 98% rebuilt yet. I am looking for a way to extract protein sequence from the rebuilt.pdb so that I could see clearly which part need to be rebuilt by sequence alignment. Any ideas about this? thanks Best Jane
Re: [ccp4bb] to extract protein sequence from a rebuilt pdb file
Thanks, I have found out that swiss pdb viewer could easily export sequence, thanks all. On Wed, Oct 1, 2008 at 5:49 PM, S. Thiyagarajan [EMAIL PROTECTED] wrote: Hi I would take it pdb deposition site (rcsb.org) and feed the pdb into the validation server. That gives out the sequence of the input pdb regards == S. Thiyagarajan == == #5344 Scott Hall == == Department of Biochemistry and Molecular Biology == == School of Medicine, Wayne State University == == 540 E. Canfield St. == == Detroit, MI 48201 U.S.A == == Phone: +1-313-577-0618 (lab) == +1-248-412-3758 (Cell) == --- On *Wed, 10/1/08, Jane Bailey [EMAIL PROTECTED]* wrote: From: Jane Bailey [EMAIL PROTECTED] Subject: [ccp4bb] to extract protein sequence from a rebuilt pdb file To: CCP4BB@JISCMAIL.AC.UK Date: Wednesday, October 1, 2008, 4:40 AM Hi, all I am currently rebuilting my structure in coot, and the protein sequence is around 98% rebuilt yet. I am looking for a way to extract protein sequence from the rebuilt.pdb so that I could see clearly which part need to be rebuilt by sequence alignment. Any ideas about this? thanks Best Jane
