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Re: [sdpd] General questions/stuck
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- Subject: Re: [sdpd] General questions/stuck
- From: Laxmi Shilpa Nethy <n_laxmishilpa...@yahoo.com>
- Date: Fri, 13 Aug 2010 10:59:18 -0700 (PDT)
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<p>hi cruz,<br>
this is shilpa,I am working in a pharma industry,in crystallography area.<br>
<br>
I am planning to try this software for pharmaceutical.is it possible? <br>
<br>
________________________________<br>
From: paula vera-cruz <<a href="mailto:pauveracruz%40gmail.com";>pauveracruz...@gmail.com</a>><br>
To: <a href="mailto:sdpd%40yahoogroups.com";>sdpd...@yahoogroups.com</a><br>
Sent: Tue, 10 August, 2010 7:33:53 PM<br>
Subject: Re: [sdpd] General questions/stuck<br>
<br>
Hi Phill,<br>
I don't have any experience with FOX or JANA2006, but I can recommend<br>
EXPO2009. I have used this programm to solve difficult structures and it is<br>
very easy and straight forward. It lets you start from scratch, index the<br>
pattern and then add the atoms in the unit cell to find space group and<br>
atomic positions.<br>
I have a few tutorials that could help you. If you decide to give it a try<br>
write to me and I will send them to you.<br>
Regarding the problem of two long lattice constants and one short one,<br>
although it is a way to know that the cell is wrongly indexed, this is not<br>
always the case. I work with MOFs and in these type of structures you often<br>
get cells where one lattice constant is significantly shorter that the<br>
others. So to know if the cell is right or wrong you need to look at similar<br>
structures and see if this could be possible. See if you can explain the<br>
short cell lattice, for example in my case I have an organic chain of 5A, so<br>
a lattice of 5A is acceptable, but anything shorter is questionable.<br>
I hope all this helps.<br>
Regards<br>
Paula<br>
<br>
2010/8/5 phillenglish7 <<a href="mailto:phillenglish7%40yahoo.com.au";>phillenglish7...@yahoo.com.au</a>><br>
<br>
><br>
><br>
> Dear SDPD group,<br>
><br>
> I stumbled onto this group from the back of the SDPD book by David et al.<br>
> and I was wondering if some of you might be able to help me some<br>
> difficulties I've been having completing a structural determination. I'm<br>
> going to try to give as much detailed info as possible to give some context<br>
> to my question, so I hope you'll forgive me if I bang on a bit. Also, this<br>
> is the first time for me posting to a mailing group, so I hope I get the<br>
> protocol right!<br>
><br>
> * I'm looking at the structure of TiOSO4.2H2O, the dihydrate in the series<br>
> of TiOSO4 and TiOSO4.H2O whose structures have been well known for some time<br>
> now. My supervisors and I are reasonably sure that the TiOSO4.2H2O will<br>
> contain the same motifs of Ti-O octahedra shared with SO4 tetrahedra as seen<br>
> in the rest of the series and in analogues of Zr and Hf (so that's our<br>
> 'chemical information').<br>
> * I've collected two sets of laboratory X-ray diffraction patterns (an old<br>
> Siemens and a newer machine installed last year at my university), two sets<br>
> of synchrotron X-ray diffraction (from the APS and the Australian<br>
> Synchrotron) and a relatively poor, but still possibly useful neutron<br>
> diffraction pattern (deuterated). We are very confident that we have<br>
> single-phase diffraction patterns.<br>
> * Following the general recipe/method for SDPD, I've obtained a unit cell<br>
> that has been indexed using multiple programs and has been verified by the<br>
> beamline scientists at the two synchrotron institutions.<br>
> * Using the 'space group explorer' in the program FOX, I've generated a<br>
> list of possible spacegroups.<br>
> * In both the FOX and JANA2006 programs, I've used the Le Bail method to<br>
> generate a list of integrated intensities to be used in the FOX, superflip<br>
> and EXPO2004 routines.<br>
><br>
> Now, at this stage I fall down a bit. Looking at other papers of<br>
> (relatively) similar structures, such as those in<br>
> <a href="http://scripts.iucr.org/cgi-bin/paper?la0055";>http://scripts.iucr.org/cgi-bin/paper?la0055</a> and<br>
> <a href="http://pubs.acs.org/doi/abs/10.1021/ic00268a025";>http://pubs.acs.org/doi/abs/10.1021/ic00268a025</a> it seems they generated a<br>
> Patterson map in order to determine the positions of heavy atoms. Now, I'm a<br>
> bit of a newbie and I cannot for the life of me figure out how they did<br>
> this. So the most basic of my questions is: how can I generate a Patterson<br>
> map in either FOX or JANA2006? JANA2006 has the option of producing a<br>
> Fourier map, but in order to do so I need to add atoms, which seems<br>
> counter-intuitive. Quite confused on this issue. :/<br>
><br>
> Detouring from Patterson maps a bit, I've also tried invoking the FOX<br>
> reverse Monte Carlo technique and the JANA2006 Superflip method, but I've<br>
> received nothing but nonsense answers thus far from them. My first thought<br>
> was that the unit cell might be incorrect, and so I checked into ways in<br>
> which indexing from a synchrotron can go wrong, and noticed a quote in the<br>
> David SDPD book about there being issues if two of the lattice constants are<br>
> very long and one is short, and the peak that has been used to determine<br>
> that short lattice constant is spurious. I have a similar situation with my<br>
> indexed unit cell, (a ~ 18Ang, b~16Ang, c~5Ang) and so was wondering how I<br>
> might check for this?<br>
><br>
> If anyone is interested enough in this problem to want to lend a helping<br>
> hand in a more direct way, feel free to contact me at<br>
> <a href="mailto:phill.english%40gmail.com";>phill.english...@gmail.com</a> <phill.english%40gmail.com> and I can provide any<br>
> data files/extra info you might need. I am entering the final stages of my<br>
> Ph.D., and while I would love to have the time to puzzle all these problems<br>
> out myself and learn from them, I'm spending more time banging my head<br>
> against walls than is useful at this point. That said, I am well aware that<br>
> all of you are professionals with your own challenges to overcome, and<br>
> demands on your time.<br>
><br>
> Thank you for your time and I hope to hear from some of you soon,<br>
><br>
> Phillip English<br>
><br>
> <br>
><br>
<br>
[Non-text portions of this message have been removed]<br>
<br>
------------------------------------<br>
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color: #1e66ae;
}
#actions {
font-family: Verdana;
font-size: 11px;
padding: 10px 0;
}
#activity {
background-color: #e0ecee;
float: left;
font-family: Verdana;
font-size: 10px;
padding: 10px;
}
#activity span {
font-weight: 700;
}
#activity span:first-child {
text-transform: uppercase;
}
#activity span a {
color: #5085b6;
text-decoration: none;
}
#activity span span {
color: #ff7900;
}
#activity span .underline {
text-decoration: underline;
}
.attach {
clear: both;
display: table;
font-family: Arial;
font-size: 12px;
padding: 10px 0;
width: 400px;
}
.attach div a {
text-decoration: none;
}
.attach img {
border: none;
padding-right: 5px;
}
.attach label {
display: block;
margin-bottom: 5px;
}
.attach label a {
text-decoration: none;
}
blockquote {
margin: 0 0 0 4px;
}
.bold {
font-family: Arial;
font-size: 13px;
font-weight: 700;
}
.bold a {
text-decoration: none;
}
dd.last p a {
font-family: Verdana;
font-weight: 700;
}
dd.last p span {
margin-right: 10px;
font-family: Verdana;
font-weight: 700;
}
dd.last p span.yshortcuts {
margin-right: 0;
}
div.attach-table div div a {
text-decoration: none;
}
div.attach-table {
width: 400px;
}
div.file-title a, div.file-title a:active, div.file-title a:hover, div.file-title a:visited {
text-decoration: none;
}
div.photo-title a, div.photo-title a:active, div.photo-title a:hover, div.photo-title a:visited {
text-decoration: none;
}
div#ygrp-mlmsg #ygrp-msg p a span.yshortcuts {
font-family: Verdana;
font-size: 10px;
font-weight: normal;
}
.green {
color: #628c2a;
}
.MsoNormal {
margin: 0 0 0 0;
}
o {
font-size: 0;
}
#photos div {
float: left;
width: 72px;
}
#photos div div {
border: 1px solid #666666;
height: 62px;
overflow: hidden;
width: 62px;
}
#photos div label {
color: #666666;
font-size: 10px;
overflow: hidden;
text-align: center;
white-space: nowrap;
width: 64px;
}
#reco-category {
font-size: 77%;
}
#reco-desc {
font-size: 77%;
}
.replbq {
margin: 4px;
}
#ygrp-actbar div a:first-child {
/* border-right: 0px solid #000;*/
margin-right: 2px;
padding-right: 5px;
}
#ygrp-mlmsg {
font-size: 13px;
font-family: Arial, helvetica,clean, sans-serif;
*font-size: small;
*font: x-small;
}
#ygrp-mlmsg table {
font-size: inherit;
font: 100%;
}
#ygrp-mlmsg select, input, textarea {
font: 99% Arial, Helvetica, clean, sans-serif;
}
#ygrp-mlmsg pre, code {
font:115% monospace;
*font-size:100%;
}
#ygrp-mlmsg * {
line-height: 1.22em;
}
#ygrp-mlmsg #logo {
padding-bottom: 10px;
}
#ygrp-mlmsg a {
color: #1E66AE;
}
#ygrp-msg p a {
font-family: Verdana;
}
#ygrp-msg p#attach-count span {
color: #1E66AE;
font-weight: 700;
}
#ygrp-reco #reco-head {
color: #ff7900;
font-weight: 700;
}
#ygrp-reco {
margin-bottom: 20px;
padding: 0px;
}
#ygrp-sponsor #ov li a {
font-size: 130%;
text-decoration: none;
}
#ygrp-sponsor #ov li {
font-size: 77%;
list-style-type: square;
padding: 6px 0;
}
#ygrp-sponsor #ov ul {
margin: 0;
padding: 0 0 0 8px;
}
#ygrp-text {
font-family: Georgia;
}
#ygrp-text p {
margin: 0 0 1em 0;
}
#ygrp-text tt {
font-size: 120%;
}
#ygrp-vital ul li:last-child {
border-right: none !important;
}
-->
</style>
</head>
<!--~-|**|PrettyHtmlEnd|**|-~-->
</html>
<!-- end group email -->
</x-html>